<?xml version="1.0" encoding="us-ascii" standalone="yes"?>
<!-- DFIN ActiveDisclosure(SM) XBRL Linkbase Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2019-08-06T22:39:57.1165134+00:00 -->
<!-- Version            : 3.6.7150.26138 -->
<!-- Package ID         : 505f1205fea74afd96f04a9698b3af75 -->
<!-- Copyright (c) 2019 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/role/TemplateLink" xlink:href="sybx-20190630.xsd#TemplateLink" xlink:type="simple" />
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DocumentDocumentAndEntityInformation" xlink:href="sybx-20190630.xsd#Role_DocumentDocumentAndEntityInformation" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DocumentDocumentAndEntityInformation">
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_LocalPhoneNumber" xlink:type="locator" xlink:label="dei_LocalPhoneNumber" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_CityAreaCode" xlink:type="locator" xlink:label="dei_CityAreaCode" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityAddressPostalZipCode" xlink:type="locator" xlink:label="dei_EntityAddressPostalZipCode" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityAddressCityOrTown" xlink:type="locator" xlink:label="dei_EntityAddressCityOrTown" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityAddressAddressLine2" xlink:type="locator" xlink:label="dei_EntityAddressAddressLine2" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityAddressAddressLine1" xlink:type="locator" xlink:label="dei_EntityAddressAddressLine1" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityTaxIdentificationNumber" xlink:type="locator" xlink:label="dei_EntityTaxIdentificationNumber" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityFileNumber" xlink:type="locator" xlink:label="dei_EntityFileNumber" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityAddressStateOrProvince" xlink:type="locator" xlink:label="dei_EntityAddressStateOrProvince" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityCommonStockSharesOutstanding" xlink:type="locator" xlink:label="dei_EntityCommonStockSharesOutstanding" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityExTransitionPeriod" xlink:type="locator" xlink:label="dei_EntityExTransitionPeriod" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityEmergingGrowthCompany" xlink:type="locator" xlink:label="dei_EntityEmergingGrowthCompany" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntitySmallBusiness" xlink:type="locator" xlink:label="dei_EntitySmallBusiness" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityShellCompany" xlink:type="locator" xlink:label="dei_EntityShellCompany" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityFilerCategory" xlink:type="locator" xlink:label="dei_EntityFilerCategory" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_CurrentFiscalYearEndDate" xlink:type="locator" xlink:label="dei_CurrentFiscalYearEndDate" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityCurrentReportingStatus" xlink:type="locator" xlink:label="dei_EntityCurrentReportingStatus" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityCentralIndexKey" xlink:type="locator" xlink:label="dei_EntityCentralIndexKey" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityRegistrantName" xlink:type="locator" xlink:label="dei_EntityRegistrantName" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_TradingSymbol" xlink:type="locator" xlink:label="dei_TradingSymbol" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_DocumentFiscalPeriodFocus" xlink:type="locator" xlink:label="dei_DocumentFiscalPeriodFocus" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_DocumentFiscalYearFocus" xlink:type="locator" xlink:label="dei_DocumentFiscalYearFocus" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_DocumentPeriodEndDate" xlink:type="locator" xlink:label="dei_DocumentPeriodEndDate" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_AmendmentFlag" xlink:type="locator" xlink:label="dei_AmendmentFlag" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_DocumentType" xlink:type="locator" xlink:label="dei_DocumentType" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_DocumentAndEntityInformationAbstract" xlink:type="locator" xlink:label="sybx_DocumentAndEntityInformationAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentType" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_AmendmentFlag" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentPeriodEndDate" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentFiscalYearFocus" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentFiscalPeriodFocus" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_TradingSymbol" order="10110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityRegistrantName" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityCentralIndexKey" order="10150.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityCurrentReportingStatus" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_CurrentFiscalYearEndDate" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityFilerCategory" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityShellCompany" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntitySmallBusiness" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityEmergingGrowthCompany" order="10270.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityExTransitionPeriod" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityCommonStockSharesOutstanding" order="10310.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityAddressStateOrProvince" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityFileNumber" order="10350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityTaxIdentificationNumber" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityAddressAddressLine1" order="10390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityAddressAddressLine2" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityAddressCityOrTown" order="10430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_EntityAddressPostalZipCode" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_CityAreaCode" order="10470.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_DocumentAndEntityInformationAbstract" xlink:to="dei_LocalPhoneNumber" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedBalanceSheetsUnaudited" xlink:href="sybx-20190630.xsd#Role_StatementConsolidatedBalanceSheetsUnaudited" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedBalanceSheetsUnaudited">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockValue" xlink:type="locator" xlink:label="us-gaap_CommonStockValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PreferredStockValue" xlink:type="locator" xlink:label="us-gaap_PreferredStockValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockholdersEquityAbstract" xlink:type="locator" xlink:label="us-gaap_StockholdersEquityAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingencies" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingencies" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LiabilitiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_LiabilitiesNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityNoncurrent" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DeferredRentCreditNoncurrent" xlink:type="locator" xlink:label="us-gaap_DeferredRentCreditNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LiabilitiesNoncurrentAbstract" xlink:type="locator" xlink:label="us-gaap_LiabilitiesNoncurrentAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DeferredRentCreditCurrent" xlink:type="locator" xlink:label="us-gaap_DeferredRentCreditCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ContractWithCustomerLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:type="locator" xlink:label="us-gaap_AccountsPayableCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LiabilitiesCurrentAbstract" xlink:type="locator" xlink:label="us-gaap_LiabilitiesCurrentAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:type="locator" xlink:label="us-gaap_LiabilitiesAndStockholdersEquityAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_Assets" xlink:type="locator" xlink:label="us-gaap_Assets" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherAssetsNoncurrent" xlink:type="locator" xlink:label="us-gaap_OtherAssetsNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedCashNoncurrent" xlink:type="locator" xlink:label="us-gaap_RestrictedCashNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AssetsCurrent" xlink:type="locator" xlink:label="us-gaap_AssetsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherAssetsCurrent" xlink:type="locator" xlink:label="us-gaap_OtherAssetsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PrepaidExpenseCurrent" xlink:type="locator" xlink:label="us-gaap_PrepaidExpenseCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AssetsCurrentAbstract" xlink:type="locator" xlink:label="us-gaap_AssetsCurrentAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AssetsAbstract" xlink:type="locator" xlink:label="us-gaap_AssetsAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementOfFinancialPositionAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_AssetsAbstract" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_AssetsCurrentAbstract" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_PrepaidExpenseCurrent" order="10530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_OtherAssetsCurrent" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_AssetsCurrent" order="10610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" order="10650.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" order="10730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_RestrictedCashNoncurrent" order="10770.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_OtherAssetsNoncurrent" order="10810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_Assets" order="10850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_LiabilitiesAndStockholdersEquityAbstract" order="10890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesCurrentAbstract" order="10970.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccountsPayableCurrent" order="11050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="11090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_ContractWithCustomerLiabilityCurrent" order="11130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_DeferredRentCreditCurrent" order="11170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" order="11210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityCurrent" order="11250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_LiabilitiesCurrent" order="11290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesNoncurrentAbstract" order="11330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_DeferredRentCreditNoncurrent" order="11410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" order="11450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityNoncurrent" order="11490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_LiabilitiesNoncurrent" order="11530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_CommitmentsAndContingencies" order="11570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_StockholdersEquityAbstract" order="11610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_PreferredStockValue" order="11690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_CommonStockValue" order="11730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_AdditionalPaidInCapitalCommonStock" order="11770.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" order="11810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="11850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityAbstract" xlink:to="us-gaap_StockholdersEquity" order="11890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesAndStockholdersEquity" order="11930.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedBalanceSheetsUnauditedParenthetical" xlink:href="sybx-20190630.xsd#Role_StatementConsolidatedBalanceSheetsUnauditedParenthetical" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedBalanceSheetsUnauditedParenthetical">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockSharesOutstanding" xlink:type="locator" xlink:label="us-gaap_CommonStockSharesOutstanding" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockSharesIssued" xlink:type="locator" xlink:label="us-gaap_CommonStockSharesIssued" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockSharesAuthorized" xlink:type="locator" xlink:label="us-gaap_CommonStockSharesAuthorized" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:type="locator" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PreferredStockSharesOutstanding" xlink:type="locator" xlink:label="us-gaap_PreferredStockSharesOutstanding" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PreferredStockSharesIssued" xlink:type="locator" xlink:label="us-gaap_PreferredStockSharesIssued" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PreferredStockSharesAuthorized" xlink:type="locator" xlink:label="us-gaap_PreferredStockSharesAuthorized" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PreferredStockParOrStatedValuePerShare" xlink:type="locator" xlink:label="us-gaap_PreferredStockParOrStatedValuePerShare" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementOfFinancialPositionAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfFinancialPositionAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_PreferredStockParOrStatedValuePerShare" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_PreferredStockSharesAuthorized" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_PreferredStockSharesIssued" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_PreferredStockSharesOutstanding" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockSharesAuthorized" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockSharesIssued" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfFinancialPositionAbstract" xlink:to="us-gaap_CommonStockSharesOutstanding" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedStatementsOfOperationsUnaudited" xlink:href="sybx-20190630.xsd#Role_StatementConsolidatedStatementsOfOperationsUnaudited" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedStatementsOfOperationsUnaudited">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:type="locator" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ComprehensiveIncomeNetOfTaxAbstract" xlink:type="locator" xlink:label="us-gaap_ComprehensiveIncomeNetOfTaxAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" xlink:type="locator" xlink:label="us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EarningsPerShareBasicAndDiluted" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareBasicAndDiluted" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NonoperatingIncomeExpense" xlink:type="locator" xlink:label="us-gaap_NonoperatingIncomeExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:type="locator" xlink:label="us-gaap_OtherNonoperatingIncomeExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InterestExpense" xlink:type="locator" xlink:label="us-gaap_InterestExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentIncomeNonoperating" xlink:type="locator" xlink:label="us-gaap_InvestmentIncomeNonoperating" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NonoperatingIncomeExpenseAbstract" xlink:type="locator" xlink:label="us-gaap_NonoperatingIncomeExpenseAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingIncomeLoss" xlink:type="locator" xlink:label="us-gaap_OperatingIncomeLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingExpenses" xlink:type="locator" xlink:label="us-gaap_OperatingExpenses" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:type="locator" xlink:label="us-gaap_GeneralAndAdministrativeExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingExpensesAbstract" xlink:type="locator" xlink:label="us-gaap_OperatingExpensesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_Revenues" xlink:type="locator" xlink:label="us-gaap_Revenues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementAbstract" xlink:type="locator" xlink:label="us-gaap_IncomeStatementAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_Revenues" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_OperatingExpensesAbstract" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingExpensesAbstract" xlink:to="us-gaap_ResearchAndDevelopmentExpense" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingExpensesAbstract" xlink:to="us-gaap_GeneralAndAdministrativeExpense" order="10440.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingExpensesAbstract" xlink:to="us-gaap_OperatingExpenses" order="10520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_OperatingIncomeLoss" order="10600.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_NonoperatingIncomeExpenseAbstract" order="10680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_InvestmentIncomeNonoperating" order="10840.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_InterestExpense" order="10920.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" order="11000.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_NonoperatingIncomeExpense" order="11080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_NetIncomeLoss" order="11160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_EarningsPerShareBasicAndDiluted" order="11240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_WeightedAverageNumberOfShareOutstandingBasicAndDiluted" order="11320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementAbstract" xlink:to="us-gaap_ComprehensiveIncomeNetOfTaxAbstract" order="11400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ComprehensiveIncomeNetOfTaxAbstract" xlink:to="us-gaap_NetIncomeLoss" order="11560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ComprehensiveIncomeNetOfTaxAbstract" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="11640.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ComprehensiveIncomeNetOfTaxAbstract" xlink:to="us-gaap_ComprehensiveIncomeNetOfTax" order="11720.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedStatementsOfStockholdersEquityUnaudited" xlink:href="sybx-20190630.xsd#Role_StatementConsolidatedStatementsOfStockholdersEquityUnaudited" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedStatementsOfStockholdersEquityUnaudited">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SharesOutstanding" xlink:type="locator" xlink:label="us-gaap_SharesOutstanding_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetIncomeLoss" xlink:type="locator" xlink:label="us-gaap_NetIncomeLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:type="locator" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" xlink:type="locator" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardForfeited" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardForfeited" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalWarrantIssued" xlink:type="locator" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalWarrantIssued" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodValueNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodValueNewIssues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CumulativeEffectOnRetainedEarningsNetOfTax1" xlink:type="locator" xlink:label="us-gaap_CumulativeEffectOnRetainedEarningsNetOfTax1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SharesOutstanding" xlink:type="locator" xlink:label="us-gaap_SharesOutstanding" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockholdersEquity" xlink:type="locator" xlink:label="us-gaap_StockholdersEquity" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementLineItems" xlink:type="locator" xlink:label="us-gaap_StatementLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccountingStandardsUpdate201409Member" xlink:type="locator" xlink:label="us-gaap_AccountingStandardsUpdate201409Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_TypeOfAdoptionMember" xlink:type="locator" xlink:label="us-gaap_TypeOfAdoptionMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:type="locator" xlink:label="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RetainedEarningsMember" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeMember" xlink:type="locator" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AdditionalPaidInCapitalMember" xlink:type="locator" xlink:label="us-gaap_AdditionalPaidInCapitalMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockMember" xlink:type="locator" xlink:label="us-gaap_CommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementTable" xlink:type="locator" xlink:label="us-gaap_StatementTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementOfStockholdersEquityAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfStockholdersEquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfStockholdersEquityAbstract" xlink:to="us-gaap_StatementTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_AdditionalPaidInCapitalMember" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_RetainedEarningsMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:to="us-gaap_TypeOfAdoptionMember" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfAdoptionMember" xlink:to="us-gaap_AccountingStandardsUpdate201409Member" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="10260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockholdersEquity" order="10270.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_SharesOutstanding" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CumulativeEffectOnRetainedEarningsNetOfTax1" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueNewIssues" order="10550.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalWarrantIssued" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardForfeited" order="10830.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" order="10970.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="11110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetIncomeLoss" order="11250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockholdersEquity_li0l2" order="11390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_SharesOutstanding_li0l2" order="11410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedStatementsOfCashFlowsUnaudited" xlink:href="sybx-20190630.xsd#Role_StatementConsolidatedStatementsOfCashFlowsUnaudited" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/StatementConsolidatedStatementsOfCashFlowsUnaudited">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InterestPaidNet" xlink:type="locator" xlink:label="us-gaap_InterestPaidNet" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AssetsAcquiredUnderFinanceLeases" xlink:type="locator" xlink:label="sybx_AssetsAcquiredUnderFinanceLeases" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses" xlink:type="locator" xlink:label="sybx_IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_CashFlowNoncashFinancingActivitiesDisclosureAbstract" xlink:type="locator" xlink:label="sybx_CashFlowNoncashFinancingActivitiesDisclosureAbstract" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AssetsAcquiredUnderOperatingLeaseObligation" xlink:type="locator" xlink:label="sybx_AssetsAcquiredUnderOperatingLeaseObligation" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments" xlink:type="locator" xlink:label="sybx_NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AllowanceForTenantImprovements" xlink:type="locator" xlink:label="sybx_AllowanceForTenantImprovements" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_CashFlowNoncashInvestingDisclosureAbstract" xlink:type="locator" xlink:label="sybx_CashFlowNoncashInvestingDisclosureAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ProceedsFromIssuanceOfWarrants" xlink:type="locator" xlink:label="us-gaap_ProceedsFromIssuanceOfWarrants" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:type="locator" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeasePrincipalPayments" xlink:type="locator" xlink:label="us-gaap_FinanceLeasePrincipalPayments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" xlink:type="locator" xlink:label="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" xlink:type="locator" xlink:label="us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncreaseDecreaseInOtherOperatingAssets" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOtherOperatingAssets" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncreaseDecreaseInDeferredLiabilities" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInDeferredLiabilities" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_IncreaseDecreaseInOperatingLeaseLiabilityAndRightOfUseAsset" xlink:type="locator" xlink:label="sybx_IncreaseDecreaseInOperatingLeaseLiabilityAndRightOfUseAsset" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncreaseDecreaseInContractWithCustomerLiability" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInContractWithCustomerLiability" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:type="locator" xlink:label="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" xlink:type="locator" xlink:label="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_GainLossOnSaleOfPropertyPlantEquipment" xlink:type="locator" xlink:label="us-gaap_GainLossOnSaleOfPropertyPlantEquipment" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DepreciationAndAmortization" xlink:type="locator" xlink:label="us-gaap_DepreciationAndAmortization" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ProfitLoss" xlink:type="locator" xlink:label="us-gaap_ProfitLoss" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:type="locator" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementOfCashFlowsAbstract" xlink:type="locator" xlink:label="us-gaap_StatementOfCashFlowsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_ProfitLoss" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_DepreciationAndAmortization" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_GainLossOnSaleOfPropertyPlantEquipment" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_ShareBasedCompensation" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" order="10530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" order="10650.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInContractWithCustomerLiability" order="10730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="sybx_IncreaseDecreaseInOperatingLeaseLiabilityAndRightOfUseAsset" order="10770.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInDeferredLiabilities" order="10810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInOtherOperatingAssets" order="10850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" order="10890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" order="10930.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" order="11010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" order="11050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="11090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" order="11130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" order="11170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_FinanceLeasePrincipalPayments" order="11250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" order="11290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_ProceedsFromIssuanceOfWarrants" order="11330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" order="11370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" order="11410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" order="11450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations_li0l2" order="11490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="sybx_CashFlowNoncashInvestingDisclosureAbstract" order="11530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CashFlowNoncashInvestingDisclosureAbstract" xlink:to="sybx_AllowanceForTenantImprovements" order="11610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CashFlowNoncashInvestingDisclosureAbstract" xlink:to="sybx_NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments" order="11650.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CashFlowNoncashInvestingDisclosureAbstract" xlink:to="sybx_AssetsAcquiredUnderOperatingLeaseObligation" order="11690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="sybx_CashFlowNoncashFinancingActivitiesDisclosureAbstract" order="11730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CashFlowNoncashFinancingActivitiesDisclosureAbstract" xlink:to="sybx_IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses" order="11810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CashFlowNoncashFinancingActivitiesDisclosureAbstract" xlink:to="sybx_AssetsAcquiredUnderFinanceLeases" order="11850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CashFlowNoncashFinancingActivitiesDisclosureAbstract" xlink:to="us-gaap_InterestPaidNet" order="11890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNatureOfBusiness" xlink:href="sybx-20190630.xsd#Role_DisclosureNatureOfBusiness" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNatureOfBusiness">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureSummaryOfSignificantAccountingPolicies" xlink:href="sybx-20190630.xsd#Role_DisclosureSummaryOfSignificantAccountingPolicies" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureSummaryOfSignificantAccountingPolicies">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SignificantAccountingPoliciesTextBlock" xlink:type="locator" xlink:label="us-gaap_SignificantAccountingPoliciesTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_SignificantAccountingPoliciesTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureFairValueOfFinancialInstruments" xlink:href="sybx-20190630.xsd#Role_DisclosureFairValueOfFinancialInstruments" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureFairValueOfFinancialInstruments">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueDisclosuresTextBlock" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_FairValueDisclosuresTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestments" xlink:href="sybx-20190630.xsd#Role_DisclosureAvailableForSaleInvestments" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestments">
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AvailableForSaleSecuritiesDisclosureTextBlock" xlink:type="locator" xlink:label="sybx_AvailableForSaleSecuritiesDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:type="locator" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:to="sybx_AvailableForSaleSecuritiesDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosurePropertyAndEquipmentNet" xlink:href="sybx-20190630.xsd#Role_DisclosurePropertyAndEquipmentNet" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosurePropertyAndEquipmentNet">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentAbstract" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentAbstract" xlink:to="us-gaap_PropertyPlantAndEquipmentDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAccruedExpenses" xlink:href="sybx-20190630.xsd#Role_DisclosureAccruedExpenses" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAccruedExpenses">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" xlink:type="locator" xlink:label="us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:type="locator" xlink:label="us-gaap_PayablesAndAccrualsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureStockholdersEquity" xlink:href="sybx-20190630.xsd#Role_DisclosureStockholdersEquity" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureStockholdersEquity">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockholdersEquityNoteDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_StockholdersEquityNoteDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EquityAbstract" xlink:type="locator" xlink:label="us-gaap_EquityAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_StockholdersEquityNoteDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlans" xlink:href="sybx-20190630.xsd#Role_DisclosureEquityBasedCompensationAndEquityIncentivePlans" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlans">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAbbvieCollaborationAgreement" xlink:href="sybx-20190630.xsd#Role_DisclosureAbbvieCollaborationAgreement" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAbbvieCollaborationAgreement">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CollaborativeArrangementDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_CollaborativeArrangementDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShare" xlink:href="sybx-20190630.xsd#Role_DisclosureNetLossPerShare" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShare">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EarningsPerShareTextBlock" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_EarningsPerShareTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingencies" xlink:href="sybx-20190630.xsd#Role_DisclosureCommitmentsAndContingencies" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingencies">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_CommitmentsAndContingenciesDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureRelatedPartyTransactions" xlink:href="sybx-20190630.xsd#Role_DisclosureRelatedPartyTransactions" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureRelatedPartyTransactions">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyTransactionsDisclosureTextBlock" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionsDisclosureTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyTransactionsAbstract" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionsAbstract" xlink:to="us-gaap_RelatedPartyTransactionsDisclosureTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesPolicies" xlink:href="sybx-20190630.xsd#Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesPolicies">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock" xlink:type="locator" xlink:label="us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_RecentlyAdoptedAccountingPronouncementsPolicyTextBlock" xlink:type="locator" xlink:label="sybx_RecentlyAdoptedAccountingPronouncementsPolicyTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ConsolidationPolicyTextBlock" xlink:type="locator" xlink:label="us-gaap_ConsolidationPolicyTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_BasisOfAccountingPolicyPolicyTextBlock" xlink:type="locator" xlink:label="us-gaap_BasisOfAccountingPolicyPolicyTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_BasisOfAccountingPolicyPolicyTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_ConsolidationPolicyTextBlock" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="sybx_RecentlyAdoptedAccountingPronouncementsPolicyTextBlock" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureFairValueOfFinancialInstrumentsTables" xlink:href="sybx-20190630.xsd#Role_DisclosureFairValueOfFinancialInstrumentsTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureFairValueOfFinancialInstrumentsTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestmentsTables" xlink:href="sybx-20190630.xsd#Role_DisclosureAvailableForSaleInvestmentsTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestmentsTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesReconciliationTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesReconciliationTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:type="locator" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:to="us-gaap_ScheduleOfAvailableForSaleSecuritiesReconciliationTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosurePropertyAndEquipmentNetTables" xlink:href="sybx-20190630.xsd#Role_DisclosurePropertyAndEquipmentNetTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosurePropertyAndEquipmentNetTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentTextBlock" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentAbstract" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentAbstract" xlink:to="us-gaap_PropertyPlantAndEquipmentTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAccruedExpensesTables" xlink:href="sybx-20190630.xsd#Role_DisclosureAccruedExpensesTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAccruedExpensesTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:type="locator" xlink:label="us-gaap_PayablesAndAccrualsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansTables" xlink:href="sybx-20190630.xsd#Role_DisclosureEquityBasedCompensationAndEquityIncentivePlansTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" xlink:type="locator" xlink:label="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_NonvestedRestrictedStockSharesActivityTableTextBlock" xlink:type="locator" xlink:label="us-gaap_NonvestedRestrictedStockSharesActivityTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationStockOptionsActivityTableTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationStockOptionsActivityTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementLineItems" xlink:type="locator" xlink:label="us-gaap_StatementLineItems" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_LongTermIncentivePlan2015And2017Member" xlink:type="locator" xlink:label="sybx_LongTermIncentivePlan2015And2017Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameDomain" xlink:type="locator" xlink:label="us-gaap_PlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameAxis" xlink:type="locator" xlink:label="us-gaap_PlanNameAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementTable" xlink:type="locator" xlink:label="us-gaap_StatementTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_StatementTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_PlanNameAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015And2017Member" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationStockOptionsActivityTableTextBlock" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NonvestedRestrictedStockSharesActivityTableTextBlock" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" order="10380.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShareTables" xlink:href="sybx-20190630.xsd#Role_DisclosureNetLossPerShareTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShareTables">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesTables" xlink:href="sybx-20190630.xsd#Role_DisclosureCommitmentsAndContingenciesTables" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesTables">
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ScheduleOfFutureMinimumLeasePaymentsUnderOperatingAndCapitalLeasesTableTextBlock" xlink:type="locator" xlink:label="sybx_ScheduleOfFutureMinimumLeasePaymentsUnderOperatingAndCapitalLeasesTableTextBlock" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_LesseeOperatingAndFinanceLeaseLiabilityMaturityTableTextBlock" xlink:type="locator" xlink:label="sybx_LesseeOperatingAndFinanceLeaseLiabilityMaturityTableTextBlock" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_LesseeWeightedAverageRemainingLeaseTermAndWeightedAverageDiscountRateTableTextBlock" xlink:type="locator" xlink:label="sybx_LesseeWeightedAverageRemainingLeaseTermAndWeightedAverageDiscountRateTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeaseCostTableTextBlock" xlink:type="locator" xlink:label="us-gaap_LeaseCostTableTextBlock" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_LeaseCostTableTextBlock" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="sybx_LesseeWeightedAverageRemainingLeaseTermAndWeightedAverageDiscountRateTableTextBlock" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="sybx_LesseeOperatingAndFinanceLeaseLiabilityMaturityTableTextBlock" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="sybx_ScheduleOfFutureMinimumLeasePaymentsUnderOperatingAndCapitalLeasesTableTextBlock" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNatureOfBusinessAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureNatureOfBusinessAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNatureOfBusinessAdditionalInformationDetail">
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" xlink:type="locator" xlink:label="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" xlink:type="locator" xlink:label="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SaleOfStockPricePerShare" xlink:type="locator" xlink:label="us-gaap_SaleOfStockPricePerShare" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:type="locator" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedCashNoncurrent" xlink:type="locator" xlink:label="us-gaap_RestrictedCashNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_MarketableSecuritiesNoncurrent" xlink:type="locator" xlink:label="us-gaap_MarketableSecuritiesNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashCashEquivalentsAndShortTermInvestments" xlink:type="locator" xlink:label="us-gaap_CashCashEquivalentsAndShortTermInvestments" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_NatureOfBusinessLineItems" xlink:type="locator" xlink:label="sybx_NatureOfBusinessLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockMember" xlink:type="locator" xlink:label="us-gaap_CommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_PreFundedWarrantsMember" xlink:type="locator" xlink:label="sybx_PreFundedWarrantsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_GinkgoBioworksIncMember" xlink:type="locator" xlink:label="sybx_GinkgoBioworksIncMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyDomain" xlink:type="locator" xlink:label="us-gaap_RelatedPartyDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_NatureOfBusinessTable" xlink:type="locator" xlink:label="sybx_NatureOfBusinessTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="sybx_NatureOfBusinessTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessTable" xlink:to="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="sybx_GinkgoBioworksIncMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessTable" xlink:to="us-gaap_ClassOfWarrantOrRightAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightAxis" xlink:to="us-gaap_ClassOfWarrantOrRightDomain" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightDomain" xlink:to="sybx_PreFundedWarrantsMember" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessTable" xlink:to="sybx_NatureOfBusinessLineItems" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_CashCashEquivalentsAndShortTermInvestments" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_MarketableSecuritiesNoncurrent" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_RestrictedCashNoncurrent" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="10530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_SaleOfStockPricePerShare" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="10610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" order="10650.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_NatureOfBusinessLineItems" xlink:to="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" order="10730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseLiability" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiability" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseOptionToExtend" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseOptionToExtend" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeasePracticalExpedientsPackage" xlink:type="locator" xlink:label="us-gaap_LeasePracticalExpedientsPackage" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccountingPoliciesAbstract" xlink:type="locator" xlink:label="us-gaap_AccountingPoliciesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_LeasePracticalExpedientsPackage" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_LesseeOperatingLeaseOptionToExtend" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AccountingPoliciesAbstract" xlink:to="us-gaap_OperatingLeaseLiability" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AssetsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_AssetsFairValueDisclosure" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_LongTermInvestmentsFairValueDisclosure" xlink:type="locator" xlink:label="sybx_LongTermInvestmentsFairValueDisclosure" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_InvestmentsFairValueDisclosure" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:type="locator" xlink:label="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_USTreasuryAndGovernmentShorttermDebtSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_USTreasuryAndGovernmentShorttermDebtSecuritiesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_MoneyMarketFundsMember" xlink:type="locator" xlink:label="us-gaap_MoneyMarketFundsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:type="locator" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CashAndCashEquivalentsAxis" xlink:type="locator" xlink:label="us-gaap_CashAndCashEquivalentsAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CorporateDebtSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_CorporateDebtSecuritiesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:type="locator" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinancialInstrumentAxis" xlink:type="locator" xlink:label="us-gaap_FinancialInstrumentAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommercialPaperMember" xlink:type="locator" xlink:label="us-gaap_CommercialPaperMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeCategorizationMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeAxis" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueInputsLevel3Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel3Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueInputsLevel2Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel2Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueInputsLevel1Member" xlink:type="locator" xlink:label="us-gaap_FairValueInputsLevel1Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueMeasurementsRecurringMember" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementsRecurringMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:type="locator" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueByMeasurementFrequencyAxis" xlink:type="locator" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:type="locator" xlink:label="sybx_FairValueAssetMeasuredOnRecurringBasisTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:type="locator" xlink:label="us-gaap_FairValueDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueDisclosuresAbstract" xlink:to="sybx_FairValueAssetMeasuredOnRecurringBasisTable" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_FairValueByMeasurementFrequencyAxis" order="10070.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementFrequencyDomain" xlink:to="us-gaap_FairValueMeasurementsRecurringMember" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="10070.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel1Member" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel2Member" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel3Member" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_InvestmentTypeAxis" order="10070.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember" order="10260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CommercialPaperMember" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_FinancialInstrumentAxis" order="10070.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_CorporateDebtSecuritiesMember" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_CashAndCashEquivalentsAxis" order="10070.08" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CashAndCashEquivalentsAxis" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" order="10400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:to="us-gaap_MoneyMarketFundsMember" order="10420.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_USTreasuryAndGovernmentShorttermDebtSecuritiesMember" order="10660.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" order="10800.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="10810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="us-gaap_InvestmentsFairValueDisclosure" order="10890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="sybx_LongTermInvestmentsFairValueDisclosure" order="11050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="us-gaap_AssetsFairValueDisclosure" order="11130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestmentsSummaryOfAvailableForSaleSecuritiesHeldDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureAvailableForSaleInvestmentsSummaryOfAvailableForSaleSecuritiesHeldDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestmentsSummaryOfAvailableForSaleSecuritiesHeldDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:type="locator" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:type="locator" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommercialPaperMember" xlink:type="locator" xlink:label="us-gaap_CommercialPaperMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeCategorizationMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentTypeAxis" xlink:type="locator" xlink:label="us-gaap_InvestmentTypeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_USGovernmentAgenciesDebtSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CorporateDebtSecuritiesMember" xlink:type="locator" xlink:label="us-gaap_CorporateDebtSecuritiesMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:type="locator" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinancialInstrumentAxis" xlink:type="locator" xlink:label="us-gaap_FinancialInstrumentAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:type="locator" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleTable" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_FinancialInstrumentAxis" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_CorporateDebtSecuritiesMember" order="10110.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" order="10150.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_InvestmentTypeAxis" order="10060.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CommercialPaperMember" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" order="10260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="10400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" order="10540.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" order="10680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestmentsAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureAvailableForSaleInvestmentsAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAvailableForSaleInvestmentsAdditionalInformationDetail">
    <link:loc xlink:href="sybx-20190630.xsd#sybx_OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" xlink:type="locator" xlink:label="sybx_OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerNumberOfPositions" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerNumberOfPositions" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionNumberOfPositions" xlink:type="locator" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionNumberOfPositions" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:type="locator" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionNumberOfPositions" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerNumberOfPositions" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:to="sybx_OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" xlink:href="sybx-20190630.xsd#Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentNet" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" xlink:type="locator" xlink:label="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentGross" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentGross" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentLineItems" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ConstructionInProgressMember" xlink:type="locator" xlink:label="us-gaap_ConstructionInProgressMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeaseholdImprovementsMember" xlink:type="locator" xlink:label="us-gaap_LeaseholdImprovementsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FurnitureAndFixturesMember" xlink:type="locator" xlink:label="us-gaap_FurnitureAndFixturesMember" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ComputerAndOfficeEquipmentMember" xlink:type="locator" xlink:label="sybx_ComputerAndOfficeEquipmentMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EquipmentMember" xlink:type="locator" xlink:label="us-gaap_EquipmentMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentTypeDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentByTypeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PropertyPlantAndEquipmentAbstract" xlink:type="locator" xlink:label="us-gaap_PropertyPlantAndEquipmentAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentAbstract" xlink:to="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" order="10040.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:to="us-gaap_PropertyPlantAndEquipmentByTypeAxis" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:to="us-gaap_PropertyPlantAndEquipmentTypeDomain" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_EquipmentMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="sybx_ComputerAndOfficeEquipmentMember" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_FurnitureAndFixturesMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_LeaseholdImprovementsMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_ConstructionInProgressMember" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:to="us-gaap_PropertyPlantAndEquipmentLineItems" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_PropertyPlantAndEquipmentGross" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedLiabilitiesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OtherAccruedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_OtherAccruedLiabilitiesCurrent" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AccruedResearchAndDevelopmentCurrent" xlink:type="locator" xlink:label="sybx_AccruedResearchAndDevelopmentCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AccruedProfessionalFeesCurrent" xlink:type="locator" xlink:label="us-gaap_AccruedProfessionalFeesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:type="locator" xlink:label="us-gaap_EmployeeRelatedLiabilitiesCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:type="locator" xlink:label="us-gaap_PayablesAndAccrualsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_EmployeeRelatedLiabilitiesCurrent" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_AccruedProfessionalFeesCurrent" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="sybx_AccruedResearchAndDevelopmentCurrent" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_OtherAccruedLiabilitiesCurrent" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PayablesAndAccrualsAbstract" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureStockholdersEquityAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureStockholdersEquityAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureStockholdersEquityAdditionalInformationDetail">
    <link:loc xlink:href="sybx-20190630.xsd#sybx_UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" xlink:type="locator" xlink:label="sybx_UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" xlink:type="locator" xlink:label="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" xlink:type="locator" xlink:label="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SaleOfStockPricePerShare" xlink:type="locator" xlink:label="us-gaap_SaleOfStockPricePerShare" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfStockLineItems" xlink:type="locator" xlink:label="us-gaap_ClassOfStockLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockMember" xlink:type="locator" xlink:label="us-gaap_CommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_PreFundedWarrantsMember" xlink:type="locator" xlink:label="sybx_PreFundedWarrantsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_GinkgoBioworksIncMember" xlink:type="locator" xlink:label="sybx_GinkgoBioworksIncMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyDomain" xlink:type="locator" xlink:label="us-gaap_RelatedPartyDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfStockByClassTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockholdersEquityNoteAbstract" xlink:type="locator" xlink:label="us-gaap_StockholdersEquityNoteAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StockholdersEquityNoteAbstract" xlink:to="us-gaap_ScheduleOfStockByClassTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="sybx_GinkgoBioworksIncMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ClassOfWarrantOrRightAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightAxis" xlink:to="us-gaap_ClassOfWarrantOrRightDomain" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightDomain" xlink:to="sybx_PreFundedWarrantsMember" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sybx_PreFundedWarrantsMember" order="10460.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="srt_RangeAxis" order="10030.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10500.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10540.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfStockByClassTable" xlink:to="us-gaap_ClassOfStockLineItems" order="10560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_SaleOfStockPricePerShare" order="10610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="10650.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" order="10730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" order="10770.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfStockLineItems" xlink:to="sybx_UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" order="10840.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureEquityBasedCompensationAndEquityIncentivePlansAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedStockMember" xlink:type="locator" xlink:label="us-gaap_RestrictedStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AwardTypeAxis" xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_LongTermIncentivePlan2015And2017Member" xlink:type="locator" xlink:label="sybx_LongTermIncentivePlan2015And2017Member" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_LongTermIncentivePlan2015Member" xlink:type="locator" xlink:label="sybx_LongTermIncentivePlan2015Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameDomain" xlink:type="locator" xlink:label="us-gaap_PlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameAxis" xlink:type="locator" xlink:label="us-gaap_PlanNameAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:type="locator" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015Member" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015And2017Member" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockMember" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" order="10350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensation" order="10510.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015And2017PlanDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015And2017PlanDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015And2017PlanDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1" xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue_li0l2" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue" xlink:type="locator" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1" xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1" xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageRemainingContractualTerm2" xlink:type="locator" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageRemainingContractualTerm2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresInPeriod" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresInPeriod" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_LongTermIncentivePlan2015And2017Member" xlink:type="locator" xlink:label="sybx_LongTermIncentivePlan2015And2017Member" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameDomain" xlink:type="locator" xlink:label="us-gaap_PlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_PlanNameAxis" xlink:type="locator" xlink:label="us-gaap_PlanNameAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:type="locator" xlink:label="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015And2017Member" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" order="10390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresInPeriod" order="10590.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber_li0l2" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" order="10790.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber" order="10890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" order="11020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" order="11120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice" order="11220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice" order="11320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice_li0l2" order="11420.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice" order="11520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice" order="11620.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageRemainingContractualTerm2" order="11750.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1" order="11790.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1" order="11810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue" order="11860.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue" order="11960.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue_li0l2" order="12060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue" order="12160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1" order="12260.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfRestrictedCommonStockActivityDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfRestrictedCommonStockActivityDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfRestrictedCommonStockActivityDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber_li0l2" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementLineItems" xlink:type="locator" xlink:label="us-gaap_StatementLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedStockMember" xlink:type="locator" xlink:label="us-gaap_RestrictedStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AwardTypeAxis" xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementTable" xlink:type="locator" xlink:label="us-gaap_StatementTable" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:type="locator" xlink:label="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:to="us-gaap_StatementTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_AwardTypeAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod" order="10350.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber_li0l2" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" order="10500.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" order="10560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue" order="10620.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue" order="10680.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue_li0l2" order="10740.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfEquityBasedCompensationExpensesDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfEquityBasedCompensationExpensesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfEquityBasedCompensationExpensesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:type="locator" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_GeneralAndAdministrativeExpenseMember" xlink:type="locator" xlink:label="us-gaap_GeneralAndAdministrativeExpenseMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:type="locator" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_IncomeStatementLocationAxis" xlink:type="locator" xlink:label="us-gaap_IncomeStatementLocationAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:type="locator" xlink:label="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_IncomeStatementLocationAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_GeneralAndAdministrativeExpenseMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfEquityBasedCompensationExpensesByAwardTypeDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfEquityBasedCompensationExpensesByAwardTypeDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureEquityBasedCompensationAndEquityIncentivePlansScheduleOfEquityBasedCompensationExpensesByAwardTypeDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:type="locator" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RestrictedStockMember" xlink:type="locator" xlink:label="us-gaap_RestrictedStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:type="locator" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AwardTypeAxis" xlink:type="locator" xlink:label="us-gaap_AwardTypeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:type="locator" xlink:label="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_AwardTypeAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_ShareBasedCompensation" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAbbvieCollaborationAgreementAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureAbbvieCollaborationAgreementAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureAbbvieCollaborationAgreementAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ContractWithCustomerLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_ContractWithCustomerLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_Revenues" xlink:type="locator" xlink:label="us-gaap_Revenues" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_MileStonePaymentOnAchievementOfRemainingMileStone" xlink:type="locator" xlink:label="sybx_MileStonePaymentOnAchievementOfRemainingMileStone" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_IncreaseInTransactionPriceOfPerformanceObligationOfSecondPhase" xlink:type="locator" xlink:label="sybx_IncreaseInTransactionPriceOfPerformanceObligationOfSecondPhase" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_InitialMilestonePaymentUponExecutionOfAmendment" xlink:type="locator" xlink:label="sybx_InitialMilestonePaymentUponExecutionOfAmendment" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_NumberOfMileStonePaymentsUnderSecondPhase" xlink:type="locator" xlink:label="sybx_NumberOfMileStonePaymentsUnderSecondPhase" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_MilestonePayments" xlink:type="locator" xlink:label="sybx_MilestonePayments" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod" xlink:type="locator" xlink:label="sybx_AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_PotentialMilestonePayment" xlink:type="locator" xlink:label="sybx_PotentialMilestonePayment" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_UpfrontPayments" xlink:type="locator" xlink:label="sybx_UpfrontPayments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:type="locator" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_IbdcoMember" xlink:type="locator" xlink:label="sybx_IbdcoMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_BusinessAcquisitionAcquireeDomain" xlink:type="locator" xlink:label="us-gaap_BusinessAcquisitionAcquireeDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_BusinessAcquisitionAxis" xlink:type="locator" xlink:label="us-gaap_BusinessAcquisitionAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AbbVieAgreementMember" xlink:type="locator" xlink:label="sybx_AbbVieAgreementMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:type="locator" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_TypeOfArrangementAxis" xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:type="locator" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sybx_AbbVieAgreementMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_BusinessAcquisitionAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_BusinessAcquisitionAxis" xlink:to="us-gaap_BusinessAcquisitionAcquireeDomain" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_BusinessAcquisitionAcquireeDomain" xlink:to="sybx_IbdcoMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" order="10900.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_UpfrontPayments" order="10910.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_PotentialMilestonePayment" order="10950.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod" order="11020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_MilestonePayments" order="11180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_NumberOfMileStonePaymentsUnderSecondPhase" order="11250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_InitialMilestonePaymentUponExecutionOfAmendment" order="11270.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_IncreaseInTransactionPriceOfPerformanceObligationOfSecondPhase" order="11320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="sybx_MileStonePaymentOnAchievementOfRemainingMileStone" order="11370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_Revenues" order="11420.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiabilityCurrent" order="11500.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShareAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureNetLossPerShareAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShareAdditionalInformationDetail">
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" xlink:type="locator" xlink:label="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementLineItems" xlink:type="locator" xlink:label="us-gaap_StatementLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockMember" xlink:type="locator" xlink:label="us-gaap_CommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_PreFundedWarrantsMember" xlink:type="locator" xlink:label="sybx_PreFundedWarrantsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementTable" xlink:type="locator" xlink:label="us-gaap_StatementTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_StatementTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_ClassOfWarrantOrRightAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightAxis" xlink:to="us-gaap_ClassOfWarrantOrRightDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightDomain" xlink:to="sybx_PreFundedWarrantsMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="10180.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" order="10270.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementLineItems" xlink:type="locator" xlink:label="us-gaap_StatementLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:type="locator" xlink:label="us-gaap_EmployeeStockOptionMember" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_UnvestedRestrictedStockAwardsMember" xlink:type="locator" xlink:label="sybx_UnvestedRestrictedStockAwardsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:type="locator" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementTable" xlink:type="locator" xlink:label="us-gaap_StatementTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EarningsPerShareAbstract" xlink:type="locator" xlink:label="us-gaap_EarningsPerShareAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_StatementTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="sybx_UnvestedRestrictedStockAwardsMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="10100.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementLineItems" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" order="10130.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformationDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseRightOfUseAsset" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseRightOfUseAsset" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasePayments" xlink:type="locator" xlink:label="us-gaap_OperatingLeasePayments" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_TermOfPriorTerminateWrittenNotice" xlink:type="locator" xlink:label="sybx_TermOfPriorTerminateWrittenNotice" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_EstimatedProjectCosts" xlink:type="locator" xlink:label="sybx_EstimatedProjectCosts" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AgreementExpirationDate" xlink:type="locator" xlink:label="sybx_AgreementExpirationDate" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_TermOfAgreement" xlink:type="locator" xlink:label="sybx_TermOfAgreement" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AccessAndUseOfSpaceUnderAgreement" xlink:type="locator" xlink:label="sybx_AccessAndUseOfSpaceUnderAgreement" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseExistenceOfOptionToTerminate" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseExistenceOfOptionToTerminate" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseRenewalTerm" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseRenewalTerm" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" xlink:type="locator" xlink:label="us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_TenantImprovementInvestmentObligation" xlink:type="locator" xlink:label="sybx_TenantImprovementInvestmentObligation" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseTermOfContract" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseTermOfContract" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_OperatingLeasesRentExpenseAnnualRentalPayments" xlink:type="locator" xlink:label="sybx_OperatingLeasesRentExpenseAnnualRentalPayments" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_RentableSpaceUnderLeaseAgreement" xlink:type="locator" xlink:label="sybx_RentableSpaceUnderLeaseAgreement" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_CommitmentsAndContingenciesLineItems" xlink:type="locator" xlink:label="sybx_CommitmentsAndContingenciesLineItems" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_AzzurGroupLimitedLiabilityCompanyMember" xlink:type="locator" xlink:label="sybx_AzzurGroupLimitedLiabilityCompanyMember" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_EntityDomain" xlink:type="locator" xlink:label="dei_EntityDomain" />
    <link:loc xlink:href="https://xbrl.sec.gov/dei/2018/dei-2018-01-31.xsd#dei_LegalEntityAxis" xlink:type="locator" xlink:label="dei_LegalEntityAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_MasterContractServicesAgreementMember" xlink:type="locator" xlink:label="sybx_MasterContractServicesAgreementMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:type="locator" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_TypeOfArrangementAxis" xlink:type="locator" xlink:label="us-gaap_TypeOfArrangementAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_CommitmentsAndContingenciesTable" xlink:type="locator" xlink:label="sybx_CommitmentsAndContingenciesTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="sybx_CommitmentsAndContingenciesTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sybx_MasterContractServicesAgreementMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesTable" xlink:to="srt_RangeAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10120.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10140.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesTable" xlink:to="dei_LegalEntityAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_EntityDomain" xlink:to="sybx_AzzurGroupLimitedLiabilityCompanyMember" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesTable" xlink:to="sybx_CommitmentsAndContingenciesLineItems" order="10360.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_RentableSpaceUnderLeaseAgreement" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_OperatingLeasesRentExpenseAnnualRentalPayments" order="10390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="us-gaap_LesseeOperatingLeaseTermOfContract" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_TenantImprovementInvestmentObligation" order="10430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="us-gaap_LesseeOperatingLeaseRenewalTerm" order="10470.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="us-gaap_LesseeOperatingLeaseExistenceOfOptionToTerminate" order="10510.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_AccessAndUseOfSpaceUnderAgreement" order="10560.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_TermOfAgreement" order="10580.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_AgreementExpirationDate" order="10600.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_EstimatedProjectCosts" order="10620.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="sybx_TermOfPriorTerminateWrittenNotice" order="10670.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="us-gaap_OperatingLeasePayments" order="10720.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_CommitmentsAndContingenciesLineItems" xlink:to="us-gaap_FinanceLeaseRightOfUseAsset" order="10790.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesComponentsOfLeaseCostForOperatingAndFinanceLeasesDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureCommitmentsAndContingenciesComponentsOfLeaseCostForOperatingAndFinanceLeasesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesComponentsOfLeaseCostForOperatingAndFinanceLeasesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LeaseCost" xlink:type="locator" xlink:label="us-gaap_LeaseCost" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_FinanceLeaseCost" xlink:type="locator" xlink:label="sybx_FinanceLeaseCost" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseInterestExpense" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseInterestExpense" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseRightOfUseAssetAmortization" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseRightOfUseAssetAmortization" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseCostAbstract" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseCostAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ShortTermLeaseCost" xlink:type="locator" xlink:label="us-gaap_ShortTermLeaseCost" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_OperatingAndVariableLeaseCost" xlink:type="locator" xlink:label="sybx_OperatingAndVariableLeaseCost" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_VariableLeaseCost" xlink:type="locator" xlink:label="us-gaap_VariableLeaseCost" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseCost" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseCost" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_OperatingLeaseCostAbstract" xlink:type="locator" xlink:label="sybx_OperatingLeaseCostAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="sybx_OperatingLeaseCostAbstract" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_OperatingLeaseCostAbstract" xlink:to="us-gaap_OperatingLeaseCost" order="10160.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_OperatingLeaseCostAbstract" xlink:to="us-gaap_VariableLeaseCost" order="10200.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_OperatingLeaseCostAbstract" xlink:to="sybx_OperatingAndVariableLeaseCost" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="sybx_OperatingLeaseCostAbstract" xlink:to="us-gaap_ShortTermLeaseCost" order="10280.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_FinanceLeaseCostAbstract" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseCostAbstract" xlink:to="us-gaap_FinanceLeaseRightOfUseAssetAmortization" order="10400.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseCostAbstract" xlink:to="us-gaap_FinanceLeaseInterestExpense" order="10440.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseCostAbstract" xlink:to="sybx_FinanceLeaseCost" order="10480.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_LeaseCost" order="10520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesSummaryOfWeightedAverageRemainingLeaseTermAndWeightedAverageDiscountRateForOperatingAndFinanceLeasesDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureCommitmentsAndContingenciesSummaryOfWeightedAverageRemainingLeaseTermAndWeightedAverageDiscountRateForOperatingAndFinanceLeasesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesSummaryOfWeightedAverageRemainingLeaseTermAndWeightedAverageDiscountRateForOperatingAndFinanceLeasesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseWeightedAverageRemainingLeaseTerm1" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseWeightedAverageRemainingLeaseTerm1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseWeightedAverageDiscountRatePercent" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseWeightedAverageDiscountRatePercent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseWeightedAverageRemainingLeaseTerm1" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseWeightedAverageRemainingLeaseTerm1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseWeightedAverageDiscountRatePercent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseWeightedAverageDiscountRatePercent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_OperatingLeaseWeightedAverageDiscountRatePercent" order="10010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_OperatingLeaseWeightedAverageRemainingLeaseTerm1" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_FinanceLeaseWeightedAverageDiscountRatePercent" order="10050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_FinanceLeaseWeightedAverageRemainingLeaseTerm1" order="10090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesSummaryOfMaturityOfLeaseLiabilitiesForOperatingAndFinanceLeasesDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureCommitmentsAndContingenciesSummaryOfMaturityOfLeaseLiabilitiesForOperatingAndFinanceLeasesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesSummaryOfMaturityOfLeaseLiabilitiesForOperatingAndFinanceLeasesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityNoncurrent" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiability" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiability" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityUndiscountedExcessAmount" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityUndiscountedExcessAmount" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDue" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueAfterYearFive" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueAfterYearFive" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueYearFive" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueYearFive" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueYearFour" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueYearFour" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueYearThree" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueYearThree" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityPaymentsDueYearTwo" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsDueYearTwo" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:type="locator" xlink:label="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseLiability" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiability" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFive" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFive" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:type="locator" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:type="locator" xlink:label="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" order="10170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFive" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeaseLiability" order="10610.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent" order="10730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" order="10770.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsRemainderOfFiscalYear" order="10850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueYearTwo" order="10890.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueYearThree" order="10930.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueYearFour" order="10970.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueYearFive" order="11010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDueAfterYearFive" order="11050.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityPaymentsDue" order="11090.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityUndiscountedExcessAmount" order="11170.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiability" order="11210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityCurrent" order="11290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_FinanceLeaseLiabilitiesPaymentsDueAbstract" xlink:to="us-gaap_FinanceLeaseLiabilityNoncurrent" order="11330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfAggregateFutureLeasePaymentsForOperatingAndCapitalLeasesDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureCommitmentsAndContingenciesScheduleOfAggregateFutureLeasePaymentsForOperatingAndCapitalLeasesDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureCommitmentsAndContingenciesScheduleOfAggregateFutureLeasePaymentsForOperatingAndCapitalLeasesDetail">
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeaseObligationsNoncurrent" xlink:type="locator" xlink:label="us-gaap_CapitalLeaseObligationsNoncurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeaseObligationsCurrent" xlink:type="locator" xlink:label="us-gaap_CapitalLeaseObligationsCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsPresentValueOfNetMinimumPayments" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsPresentValueOfNetMinimumPayments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsInterestIncludedInPayments" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsInterestIncludedInPayments" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDue" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueThereafter" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueThereafter" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFiveYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFiveYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFourYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFourYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInThreeYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInThreeYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueInTwoYears" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInTwoYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsDueCurrent" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsDueCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:type="locator" xlink:label="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDue" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueThereafter" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueThereafter" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFiveYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFiveYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFourYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFourYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInThreeYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInThreeYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueInTwoYears" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInTwoYears" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueCurrent" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueCurrent" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:type="locator" xlink:label="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:type="locator" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" order="10150.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueCurrent" order="10190.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInTwoYears" order="10210.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInThreeYears" order="10230.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFourYears" order="10250.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueInFiveYears" order="10270.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDueThereafter" order="10290.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OperatingLeasesFutureMinimumPaymentsDueAbstract" xlink:to="us-gaap_OperatingLeasesFutureMinimumPaymentsDue" order="10310.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" order="10330.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueCurrent" order="10370.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInTwoYears" order="10390.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInThreeYears" order="10410.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFourYears" order="10430.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueInFiveYears" order="10450.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDueThereafter" order="10470.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsDue" order="10490.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CapitalLeasesFutureMinimumPaymentsNetPresentValueAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsInterestIncludedInPayments" order="10510.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_CapitalLeasesFutureMinimumPaymentsPresentValueOfNetMinimumPayments" order="10530.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_CapitalLeaseObligationsCurrent" order="10570.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_CapitalLeaseObligationsNoncurrent" order="10590.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
  <link:roleRef roleURI="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureRelatedPartyTransactionsAdditionalInformationDetail" xlink:href="sybx-20190630.xsd#Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail" xlink:type="simple" />
  <link:presentationLink xlink:type="extended" xlink:role="http://www.synlogictx.com/20190630/taxonomy/role/DisclosureRelatedPartyTransactionsAdditionalInformationDetail">
    <link:loc xlink:href="sybx-20190630.xsd#sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" xlink:type="locator" xlink:label="sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_PrepaymentToRelatedPartyForCollaborationAgreement" xlink:type="locator" xlink:label="sybx_PrepaymentToRelatedPartyForCollaborationAgreement" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" xlink:type="locator" xlink:label="sybx_UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" xlink:type="locator" xlink:label="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" xlink:type="locator" xlink:label="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:type="locator" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyTransactionLineItems" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionLineItems" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MinimumMember" xlink:type="locator" xlink:label="srt_MinimumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_MaximumMember" xlink:type="locator" xlink:label="srt_MaximumMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeMember" xlink:type="locator" xlink:label="srt_RangeMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/srt/2018/elts/srt-2018-01-31.xsd#srt_RangeAxis" xlink:type="locator" xlink:label="srt_RangeAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_CommonStockMember" xlink:type="locator" xlink:label="us-gaap_CommonStockMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_EquityComponentDomain" xlink:type="locator" xlink:label="us-gaap_EquityComponentDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:type="locator" xlink:label="us-gaap_StatementEquityComponentsAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_PreFundedWarrantsMember" xlink:type="locator" xlink:label="sybx_PreFundedWarrantsMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:type="locator" xlink:label="us-gaap_ClassOfWarrantOrRightAxis" />
    <link:loc xlink:href="sybx-20190630.xsd#sybx_GinkgoBioworksIncMember" xlink:type="locator" xlink:label="sybx_GinkgoBioworksIncMember" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyDomain" xlink:type="locator" xlink:label="us-gaap_RelatedPartyDomain" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:type="locator" xlink:label="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" />
    <link:loc xlink:href="http://xbrl.fasb.org/us-gaap/2018/elts/us-gaap-2018-01-31.xsd#us-gaap_RelatedPartyTransactionsAbstract" xlink:type="locator" xlink:label="us-gaap_RelatedPartyTransactionsAbstract" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionsAbstract" xlink:to="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" order="10020.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" order="10030.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain" order="10060.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="sybx_GinkgoBioworksIncMember" order="10080.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_ClassOfWarrantOrRightAxis" order="10030.02" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightAxis" xlink:to="us-gaap_ClassOfWarrantOrRightDomain" order="10220.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ClassOfWarrantOrRightDomain" xlink:to="sybx_PreFundedWarrantsMember" order="10240.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="10030.04" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="10320.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="10340.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityComponentDomain" xlink:to="sybx_PreFundedWarrantsMember" order="10460.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="srt_RangeAxis" order="10030.06" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" order="10500.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" order="10520.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" order="10540.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_RelatedPartyTransactionLineItems" order="10640.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" order="10650.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" order="10690.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="10730.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" order="10810.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" order="10850.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="sybx_UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" order="10920.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="sybx_PrepaymentToRelatedPartyForCollaborationAgreement" order="10970.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" order="11010.00" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </link:presentationLink>
</link:linkbase>
