<?xml version="1.0" encoding="US-ASCII"?>
<!-- DFIN New ActiveDisclosure (SM) XBRL Linkbase Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date :2022-11-09T22:46:04.2626+00:00 -->
<!-- Copyright (c) 2022 Donnelly Financial Solutions, Inc. All Rights Reserved. -->
<link:linkbase xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" 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">
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DocumentDocumentAndEntityInformation" xlink:href="sybx-20220930.xsd#Role_DocumentDocumentAndEntityInformation" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedBalanceSheetsUnaudited" xlink:href="sybx-20220930.xsd#Role_StatementConsolidatedBalanceSheetsUnaudited" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedBalanceSheetsUnauditedParenthetical" xlink:href="sybx-20220930.xsd#Role_StatementConsolidatedBalanceSheetsUnauditedParenthetical" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedStatementsOfOperationsAndComprehensiveLossUnaudited" xlink:href="sybx-20220930.xsd#Role_StatementConsolidatedStatementsOfOperationsAndComprehensiveLossUnaudited" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedStatementsOfStockholdersEquityUnaudited" xlink:href="sybx-20220930.xsd#Role_StatementConsolidatedStatementsOfStockholdersEquityUnaudited" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedStatementsOfCashFlowsUnaudited" xlink:href="sybx-20220930.xsd#Role_StatementConsolidatedStatementsOfCashFlowsUnaudited" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNatureOfBusiness" xlink:href="sybx-20220930.xsd#Role_DisclosureNatureOfBusiness" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPolicies" xlink:href="sybx-20220930.xsd#Role_DisclosureSummaryOfSignificantAccountingPolicies" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureFairValueOfFinancialInstruments" xlink:href="sybx-20220930.xsd#Role_DisclosureFairValueOfFinancialInstruments" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestments" xlink:href="sybx-20220930.xsd#Role_DisclosureAvailableForSaleInvestments" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosurePropertyAndEquipmentNet" xlink:href="sybx-20220930.xsd#Role_DisclosurePropertyAndEquipmentNet" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAccruedExpenses" xlink:href="sybx-20220930.xsd#Role_DisclosureAccruedExpenses" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquity" xlink:href="sybx-20220930.xsd#Role_DisclosureStockholdersEquity" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensation" xlink:href="sybx-20220930.xsd#Role_DisclosureEquityBasedCompensation" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCollaborationAgreements" xlink:href="sybx-20220930.xsd#Role_DisclosureCollaborationAgreements" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShare" xlink:href="sybx-20220930.xsd#Role_DisclosureNetLossPerShare" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCommitmentsAndContingencies" xlink:href="sybx-20220930.xsd#Role_DisclosureCommitmentsAndContingencies" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureRelatedPartyTransactions" xlink:href="sybx-20220930.xsd#Role_DisclosureRelatedPartyTransactions" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies" xlink:href="sybx-20220930.xsd#Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureFairValueOfFinancialInstrumentsTables" xlink:href="sybx-20220930.xsd#Role_DisclosureFairValueOfFinancialInstrumentsTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestmentsTables" xlink:href="sybx-20220930.xsd#Role_DisclosureAvailableForSaleInvestmentsTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetTables" xlink:href="sybx-20220930.xsd#Role_DisclosurePropertyAndEquipmentNetTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAccruedExpensesTables" xlink:href="sybx-20220930.xsd#Role_DisclosureAccruedExpensesTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquityTables" xlink:href="sybx-20220930.xsd#Role_DisclosureStockholdersEquityTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationTables" xlink:href="sybx-20220930.xsd#Role_DisclosureEquityBasedCompensationTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShareTables" xlink:href="sybx-20220930.xsd#Role_DisclosureNetLossPerShareTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNatureOfBusinessAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureNatureOfBusinessAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestmentsSummaryOfAvailableForSaleSecuritiesHeldDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureAvailableForSaleInvestmentsSummaryOfAvailableForSaleSecuritiesHeldDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestmentsAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureAvailableForSaleInvestmentsAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" xlink:href="sybx-20220930.xsd#Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquityAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureStockholdersEquityAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquityScheduleOfSharesOfCommonStockReservedForFutureIssuanceDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureStockholdersEquityScheduleOfSharesOfCommonStockReservedForFutureIssuanceDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureEquityBasedCompensationAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationScheduleOfEquityBasedCompensationExpensesDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureEquityBasedCompensationScheduleOfEquityBasedCompensationExpensesDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationScheduleOfEquityBasedCompensationExpensesByAwardTypeDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureEquityBasedCompensationScheduleOfEquityBasedCompensationExpensesByAwardTypeDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCollaborationAgreementsAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureCollaborationAgreementsAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShareAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureNetLossPerShareAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail" xlink:href="sybx-20220930.xsd#Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail" xlink:type="simple"/>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DocumentDocumentAndEntityInformation" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_CoverAbstract" xlink:label="dei_CoverAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_DocumentType" xlink:label="dei_DocumentType"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_AmendmentFlag" xlink:label="dei_AmendmentFlag"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_DocumentPeriodEndDate" xlink:label="dei_DocumentPeriodEndDate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_DocumentFiscalYearFocus" xlink:label="dei_DocumentFiscalYearFocus"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_DocumentFiscalPeriodFocus" xlink:label="dei_DocumentFiscalPeriodFocus"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_TradingSymbol" xlink:label="dei_TradingSymbol"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityRegistrantName" xlink:label="dei_EntityRegistrantName"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_SecurityExchangeName" xlink:label="dei_SecurityExchangeName"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityCentralIndexKey" xlink:label="dei_EntityCentralIndexKey"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityCurrentReportingStatus" xlink:label="dei_EntityCurrentReportingStatus"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_CurrentFiscalYearEndDate" xlink:label="dei_CurrentFiscalYearEndDate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityFilerCategory" xlink:label="dei_EntityFilerCategory"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityShellCompany" xlink:label="dei_EntityShellCompany"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntitySmallBusiness" xlink:label="dei_EntitySmallBusiness"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityEmergingGrowthCompany" xlink:label="dei_EntityEmergingGrowthCompany"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_Security12bTitle" xlink:label="dei_Security12bTitle"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityCommonStockSharesOutstanding" xlink:label="dei_EntityCommonStockSharesOutstanding"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityAddressStateOrProvince" xlink:label="dei_EntityAddressStateOrProvince"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityFileNumber" xlink:label="dei_EntityFileNumber"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityIncorporationStateCountryCode" xlink:label="dei_EntityIncorporationStateCountryCode"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityTaxIdentificationNumber" xlink:label="dei_EntityTaxIdentificationNumber"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityAddressAddressLine1" xlink:label="dei_EntityAddressAddressLine1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityAddressAddressLine2" xlink:label="dei_EntityAddressAddressLine2"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityAddressCityOrTown" xlink:label="dei_EntityAddressCityOrTown"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityAddressPostalZipCode" xlink:label="dei_EntityAddressPostalZipCode"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_CityAreaCode" xlink:label="dei_CityAreaCode"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_LocalPhoneNumber" xlink:label="dei_LocalPhoneNumber"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityInteractiveDataCurrent" xlink:label="dei_EntityInteractiveDataCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_DocumentQuarterlyReport" xlink:label="dei_DocumentQuarterlyReport"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_DocumentTransitionReport" xlink:label="dei_DocumentTransitionReport"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_CoverAbstract" xlink:to="dei_DocumentType" order="0" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_AmendmentFlag" order="1" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_DocumentPeriodEndDate" order="2" 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="dei_CoverAbstract" xlink:to="dei_DocumentFiscalYearFocus" order="3" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_DocumentFiscalPeriodFocus" order="4" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_TradingSymbol" order="5" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityRegistrantName" order="6" 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="dei_CoverAbstract" xlink:to="dei_SecurityExchangeName" order="7" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityCentralIndexKey" order="8" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityCurrentReportingStatus" order="9" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_CurrentFiscalYearEndDate" order="10" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityFilerCategory" order="11" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityShellCompany" order="12" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntitySmallBusiness" order="13" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityEmergingGrowthCompany" order="14" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_Security12bTitle" order="15" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityCommonStockSharesOutstanding" order="16" 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="dei_CoverAbstract" xlink:to="dei_EntityAddressStateOrProvince" order="17" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityFileNumber" order="18" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityIncorporationStateCountryCode" order="19" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityTaxIdentificationNumber" order="20" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityAddressAddressLine1" order="21" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityAddressAddressLine2" order="22" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityAddressCityOrTown" order="23" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityAddressPostalZipCode" order="24" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_CityAreaCode" order="25" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_LocalPhoneNumber" order="26" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_EntityInteractiveDataCurrent" order="27" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_DocumentQuarterlyReport" order="28" priority="2" use="optional" preferredLabel="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_CoverAbstract" xlink:to="dei_DocumentTransitionReport" order="29" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedBalanceSheetsUnaudited" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementOfFinancialPositionAbstract" xlink:label="us-gaap_StatementOfFinancialPositionAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AssetsAbstract" xlink:label="us-gaap_AssetsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AssetsCurrentAbstract" xlink:label="us-gaap_AssetsCurrentAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:label="us-gaap_LiabilitiesAndStockholdersEquityAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesCurrentAbstract" xlink:label="us-gaap_LiabilitiesCurrentAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountsPayableCurrent" xlink:label="us-gaap_AccountsPayableCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesNoncurrentAbstract" xlink:label="us-gaap_LiabilitiesNoncurrentAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockholdersEquityAbstract" xlink:label="us-gaap_StockholdersEquityAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FinanceLeaseLiabilityNoncurrent" xlink:label="us-gaap_FinanceLeaseLiabilityNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdditionalPaidInCapitalCommonStock" xlink:label="us-gaap_AdditionalPaidInCapitalCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountsReceivableNetCurrent" xlink:label="us-gaap_AccountsReceivableNetCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ContractWithCustomerLiabilityCurrent" xlink:label="us-gaap_ContractWithCustomerLiabilityCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesNoncurrent" xlink:label="us-gaap_LiabilitiesNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommitmentsAndContingencies" xlink:label="us-gaap_CommitmentsAndContingencies"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AssetsCurrent" xlink:label="us-gaap_AssetsCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedCashNoncurrent" xlink:label="us-gaap_RestrictedCashNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FinanceLeaseLiabilityCurrent" xlink:label="us-gaap_FinanceLeaseLiabilityCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_PrepaidResearchAndDevelopmentNoncurrent" xlink:label="sybx_PrepaidResearchAndDevelopmentNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LiabilitiesCurrent" xlink:label="us-gaap_LiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherAssetsNoncurrent" xlink:label="us-gaap_OtherAssetsNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_Assets" xlink:label="us-gaap_Assets"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" order="1" priority="2" use="optional" preferredLabel="http://www.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_LiabilitiesAndStockholdersEquityAbstract" order="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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_LiabilitiesNoncurrentAbstract" order="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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_AccountsReceivableNetCurrent" order="2" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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="2" 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="2" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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_PrepaidExpenseAndOtherAssetsCurrent" order="3" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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="4" 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_RestrictedCashNoncurrent" order="4" priority="2" use="optional" preferredLabel="http://www.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="4" priority="2" use="optional" preferredLabel="http://www.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="4" 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="4" 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="sybx_PrepaidResearchAndDevelopmentNoncurrent" order="5" priority="2" use="optional" preferredLabel="http://www.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="5" 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_OtherAssetsNoncurrent" order="6" priority="2" use="optional" preferredLabel="http://www.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="7" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedBalanceSheetsUnauditedParenthetical" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementOfFinancialPositionAbstract" xlink:label="us-gaap_StatementOfFinancialPositionAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockSharesAuthorized" xlink:label="us-gaap_CommonStockSharesAuthorized"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockSharesIssued" xlink:label="us-gaap_CommonStockSharesIssued"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockSharesOutstanding" xlink:label="us-gaap_CommonStockSharesOutstanding"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedStatementsOfOperationsAndComprehensiveLossUnaudited" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementAbstract" xlink:label="us-gaap_IncomeStatementAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_Revenues" xlink:label="us-gaap_Revenues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingExpensesAbstract" xlink:label="us-gaap_OperatingExpensesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:label="us-gaap_ResearchAndDevelopmentExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NonoperatingIncomeExpenseAbstract" xlink:label="us-gaap_NonoperatingIncomeExpenseAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentIncomeNonoperating" xlink:label="us-gaap_InvestmentIncomeNonoperating"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ComprehensiveIncomeNetOfTaxAbstract" xlink:label="us-gaap_ComprehensiveIncomeNetOfTaxAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_GeneralAndAdministrativeExpense" xlink:label="us-gaap_GeneralAndAdministrativeExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InterestExpense" xlink:label="us-gaap_InterestExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingExpenses" xlink:label="us-gaap_OperatingExpenses"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingIncomeLoss" xlink:label="us-gaap_OperatingIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:label="us-gaap_OtherNonoperatingIncomeExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NonoperatingIncomeExpense" xlink:label="us-gaap_NonoperatingIncomeExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss_4"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EarningsPerShareBasic" xlink:label="us-gaap_EarningsPerShareBasic"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EarningsPerShareDiluted" xlink:label="us-gaap_EarningsPerShareDiluted"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_WeightedAverageNumberOfSharesOutstandingBasic" xlink:label="us-gaap_WeightedAverageNumberOfSharesOutstandingBasic"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding" xlink:label="us-gaap_WeightedAverageNumberOfDilutedSharesOutstanding"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_IncomeStatementAbstract" xlink:to="us-gaap_OperatingExpensesAbstract" order="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="1" 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_ComprehensiveIncomeNetOfTaxAbstract" xlink:to="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" order="1" 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_OperatingExpensesAbstract" xlink:to="us-gaap_OperatingExpenses" order="2" 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="2" 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_NonoperatingIncomeExpenseAbstract" xlink:to="us-gaap_OtherNonoperatingIncomeExpense" order="2" priority="2" use="optional" preferredLabel="http://www.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_ComprehensiveIncomeNetOfTax" order="2" 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="3" priority="2" use="optional" preferredLabel="http://www.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="3" 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_4" order="4" 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_EarningsPerShareBasic" order="5" priority="2" use="optional" preferredLabel="http://www.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_EarningsPerShareDiluted" order="6" priority="2" use="optional" preferredLabel="http://www.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_WeightedAverageNumberOfSharesOutstandingBasic" order="7" priority="2" use="optional" preferredLabel="http://www.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_WeightedAverageNumberOfDilutedSharesOutstanding" order="8" priority="2" use="optional" preferredLabel="http://www.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="9" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedStatementsOfStockholdersEquityUnaudited" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementOfStockholdersEquityAbstract" xlink:label="us-gaap_StatementOfStockholdersEquityAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AtTheMarketOfferingMember" xlink:label="sybx_AtTheMarketOfferingMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdditionalPaidInCapitalMember" xlink:label="us-gaap_AdditionalPaidInCapitalMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharesOutstanding" xlink:label="us-gaap_SharesOutstanding"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeMember" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RetainedEarningsMember" xlink:label="us-gaap_RetainedEarningsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan" xlink:label="us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" xlink:label="us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodValueNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodValueNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodValueRestrictedStockAwardGross" xlink:label="us-gaap_StockIssuedDuringPeriodValueRestrictedStockAwardGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardGross" xlink:label="us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockValueSharesIssuedNetOfTaxWithholdings" xlink:label="us-gaap_RestrictedStockValueSharesIssuedNetOfTaxWithholdings"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockSharesIssuedNetOfSharesForTaxWithholdings" xlink:label="us-gaap_RestrictedStockSharesIssuedNetOfSharesForTaxWithholdings"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardForfeited" xlink:label="us-gaap_StockIssuedDuringPeriodSharesRestrictedStockAwardForfeited"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax" xlink:label="us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodNetOfTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity_16"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharesOutstanding" xlink:label="us-gaap_SharesOutstanding_17"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="sybx_AtTheMarketOfferingMember" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_EquityComponentDomain" xlink:to="us-gaap_AdditionalPaidInCapitalMember" order="1" priority="2" use="optional" preferredLabel="http://www.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_SubsidiarySaleOfStockAxis" order="1" priority="2" use="optional" preferredLabel="http://www.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_SharesOutstanding" order="1" 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_EquityComponentDomain" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeMember" order="2" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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_StockIssuedDuringPeriodValueStockOptionsExercised" order="2" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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_StockIssuedDuringPeriodSharesStockOptionsExercised" order="3" priority="2" use="optional" preferredLabel="http://www.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_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan" order="4" priority="2" use="optional" preferredLabel="http://www.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_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" order="5" priority="2" use="optional" preferredLabel="http://www.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="6" priority="2" use="optional" preferredLabel="http://www.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="7" priority="2" use="optional" preferredLabel="http://www.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_StockIssuedDuringPeriodValueRestrictedStockAwardGross" order="8" priority="2" use="optional" preferredLabel="http://www.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_StockIssuedDuringPeriodSharesRestrictedStockAwardGross" order="9" priority="2" use="optional" preferredLabel="http://www.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_RestrictedStockValueSharesIssuedNetOfTaxWithholdings" order="10" priority="2" use="optional" preferredLabel="http://www.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_RestrictedStockSharesIssuedNetOfSharesForTaxWithholdings" order="11" 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_StockIssuedDuringPeriodSharesRestrictedStockAwardForfeited" order="12" 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="13" priority="2" use="optional" preferredLabel="http://www.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="14" priority="2" use="optional" preferredLabel="http://www.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="15" priority="2" use="optional" preferredLabel="http://www.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_16" order="16" 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_17" order="17" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_StatementConsolidatedStatementsOfCashFlowsUnaudited" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementOfCashFlowsAbstract" xlink:label="us-gaap_StatementOfCashFlowsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AtTheMarketOfferingMember" xlink:label="sybx_AtTheMarketOfferingMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivitiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProfitLoss" xlink:label="us-gaap_ProfitLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract" xlink:label="us-gaap_AdjustmentsToReconcileNetIncomeLossToCashProvidedByUsedInOperatingActivitiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_Depreciation" xlink:label="us-gaap_Depreciation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivitiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt" xlink:label="us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivitiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FinanceLeasePrincipalPayments" xlink:label="us-gaap_FinanceLeasePrincipalPayments"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_NoncashInvestingItemsAbstract" xlink:label="sybx_NoncashInvestingItemsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AssetsAcquiredUnderOperatingLeaseObligation" xlink:label="sybx_AssetsAcquiredUnderOperatingLeaseObligation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInOperatingCapitalAbstract" xlink:label="us-gaap_IncreaseDecreaseInOperatingCapitalAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:label="us-gaap_IncreaseDecreaseInAccountsReceivable"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_NoncashFinancingItemsAbstract" xlink:label="sybx_NoncashFinancingItemsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CapitalLeaseObligationsIncurred" xlink:label="us-gaap_CapitalLeaseObligationsIncurred"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromSaleAndMaturityOfMarketableSecurities" xlink:label="us-gaap_ProceedsFromSaleAndMaturityOfMarketableSecurities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments" xlink:label="sybx_NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses" xlink:label="sybx_IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments" xlink:label="us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_IncreaseDecreaseInPrepaidResearchAndDevelopmentNetOfCurrentPortion" xlink:label="sybx_IncreaseDecreaseInPrepaidResearchAndDevelopmentNetOfCurrentPortion"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" xlink:label="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ProceedsFromEmployeeStockPurchasesAndExerciseOfStockOptions" xlink:label="sybx_ProceedsFromEmployeeStockPurchasesAndExerciseOfStockOptions"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InterestPaidNet" xlink:label="us-gaap_InterestPaidNet"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ChangeInCarryingAmountOfOperatingLeaseRightOfUseAsset" xlink:label="sybx_ChangeInCarryingAmountOfOperatingLeaseRightOfUseAsset"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" xlink:label="us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInContractWithCustomerLiability" xlink:label="us-gaap_IncreaseDecreaseInContractWithCustomerLiability"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations_5"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInOperatingLeaseLiability" xlink:label="us-gaap_IncreaseDecreaseInOperatingLeaseLiability"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncreaseDecreaseInOtherOperatingAssets" xlink:label="us-gaap_IncreaseDecreaseInOtherOperatingAssets"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_StatementOfCashFlowsAbstract" xlink:to="us-gaap_StatementTable" order="0" priority="2" use="optional" preferredLabel="http://www.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_SubsidiarySaleOfStockAxis" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="sybx_AtTheMarketOfferingMember" order="0" priority="2" use="optional" preferredLabel="http://www.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_NetCashProvidedByUsedInOperatingActivitiesAbstract" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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_Depreciation" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_FinanceLeasePrincipalPayments" order="0" 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="sybx_NoncashInvestingItemsAbstract" xlink:to="sybx_AssetsAcquiredUnderOperatingLeaseObligation" order="0" priority="2" use="optional" preferredLabel="http://www.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_IncreaseDecreaseInAccountsReceivable" order="0" 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="sybx_NoncashFinancingItemsAbstract" xlink:to="us-gaap_CapitalLeaseObligationsIncurred" order="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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_ShareBasedCompensation" order="1" priority="2" use="optional" preferredLabel="http://www.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="1" 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_NetCashProvidedByUsedInInvestingActivitiesAbstract" order="1" priority="2" use="optional" preferredLabel="http://www.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_ProceedsFromSaleAndMaturityOfMarketableSecurities" order="1" priority="2" use="optional" preferredLabel="http://www.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_ProceedsFromIssuanceOfCommonStock" order="1" priority="2" use="optional" preferredLabel="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_NoncashInvestingItemsAbstract" xlink:to="sybx_NoncashPurchaseOfPropertyPlantAndEquipmentInAccountsPayableAndAccruedLiabilitiesAdjustments" order="1" priority="2" use="optional" preferredLabel="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_NoncashFinancingItemsAbstract" xlink:to="sybx_IssuanceCostsIncludedInAccountsPayableAndAccruedExpenses" order="1" priority="2" use="optional" preferredLabel="http://www.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="2" 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_IncreaseDecreaseInOperatingCapitalAbstract" order="2" priority="2" use="optional" preferredLabel="http://www.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_IncreaseDecreaseInPrepaidResearchAndDevelopmentNetOfCurrentPortion" order="2" priority="2" use="optional" preferredLabel="http://www.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_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" order="2" priority="2" use="optional" preferredLabel="http://www.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_NetCashProvidedByUsedInFinancingActivitiesAbstract" order="2" priority="2" use="optional" preferredLabel="http://www.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="sybx_ProceedsFromEmployeeStockPurchasesAndExerciseOfStockOptions" order="2" priority="2" use="optional" preferredLabel="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_NoncashFinancingItemsAbstract" xlink:to="us-gaap_InterestPaidNet" order="2" priority="2" use="optional" preferredLabel="http://www.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="sybx_ChangeInCarryingAmountOfOperatingLeaseRightOfUseAsset" order="3" priority="2" use="optional" preferredLabel="http://www.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_IncreaseDecreaseInAccountsPayableAndAccruedLiabilities" order="3" priority="2" use="optional" preferredLabel="http://www.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_NetCashProvidedByUsedInOperatingActivities" order="3" 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_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" order="3" 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_PaymentsRelatedToTaxWithholdingForShareBasedCompensation" order="3" 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_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect" order="3" 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_NetCashProvidedByUsedInInvestingActivitiesAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities" order="4" 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_NetCashProvidedByUsedInFinancingActivitiesAbstract" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities" order="4" 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_StatementLineItems" xlink:to="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations" order="4" 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_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInContractWithCustomerLiability" order="4" priority="2" use="optional" preferredLabel="http://www.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_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsIncludingDisposalGroupAndDiscontinuedOperations_5" order="5" 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_IncreaseDecreaseInOperatingCapitalAbstract" xlink:to="us-gaap_IncreaseDecreaseInOperatingLeaseLiability" order="5" priority="2" use="optional" preferredLabel="http://www.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_NoncashInvestingItemsAbstract" order="6" priority="2" use="optional" preferredLabel="http://www.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="6" 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="sybx_NoncashFinancingItemsAbstract" order="7" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNatureOfBusiness" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPolicies" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingPoliciesAbstract" xlink:label="us-gaap_AccountingPoliciesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SignificantAccountingPoliciesTextBlock" xlink:label="us-gaap_SignificantAccountingPoliciesTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureFairValueOfFinancialInstruments" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:label="us-gaap_FairValueDisclosuresAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueDisclosuresTextBlock" xlink:label="us-gaap_FairValueDisclosuresTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestments" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AvailableForSaleSecuritiesDisclosureTextBlock" xlink:label="sybx_AvailableForSaleSecuritiesDisclosureTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosurePropertyAndEquipmentNet" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentAbstract" xlink:label="us-gaap_PropertyPlantAndEquipmentAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentDisclosureTextBlock" xlink:label="us-gaap_PropertyPlantAndEquipmentDisclosureTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAccruedExpenses" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:label="us-gaap_PayablesAndAccrualsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" xlink:label="us-gaap_AccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquity" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityAbstract" xlink:label="us-gaap_EquityAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockholdersEquityNoteDisclosureTextBlock" xlink:label="us-gaap_StockholdersEquityNoteDisclosureTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensation" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCollaborationAgreements" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CollaborativeArrangementDisclosureTextBlock" xlink:label="us-gaap_CollaborativeArrangementDisclosureTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShare" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EarningsPerShareAbstract" xlink:label="us-gaap_EarningsPerShareAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EarningsPerShareTextBlock" xlink:label="us-gaap_EarningsPerShareTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCommitmentsAndContingencies" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommitmentsAndContingenciesDisclosureTextBlock" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureRelatedPartyTransactions" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsAbstract" xlink:label="us-gaap_RelatedPartyTransactionsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsDisclosureTextBlock" xlink:label="us-gaap_RelatedPartyTransactionsDisclosureTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesPolicies" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingPoliciesAbstract" xlink:label="us-gaap_AccountingPoliciesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BasisOfAccountingPolicyPolicyTextBlock" xlink:label="us-gaap_BasisOfAccountingPolicyPolicyTextBlock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ConsolidationPolicyTextBlock" xlink:label="us-gaap_ConsolidationPolicyTextBlock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock" xlink:label="us-gaap_NewAccountingPronouncementsPolicyPolicyTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureFairValueOfFinancialInstrumentsTables" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:label="us-gaap_FairValueDisclosuresAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock" xlink:label="us-gaap_ScheduleOfFairValueAssetsAndLiabilitiesMeasuredOnRecurringBasisTableTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestmentsTables" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesReconciliationTableTextBlock" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesReconciliationTableTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetTables" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentAbstract" xlink:label="us-gaap_PropertyPlantAndEquipmentAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentTextBlock" xlink:label="us-gaap_PropertyPlantAndEquipmentTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAccruedExpensesTables" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:label="us-gaap_PayablesAndAccrualsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock" xlink:label="us-gaap_ScheduleOfAccruedLiabilitiesTableTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquityTables" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityAbstract" xlink:label="us-gaap_EquityAbstract"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ScheduleOfSharesOfCommonStockReservedForFutureIssuanceTableTextBlock" xlink:label="sybx_ScheduleOfSharesOfCommonStockReservedForFutureIssuanceTableTextBlock"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="sybx_ScheduleOfSharesOfCommonStockReservedForFutureIssuanceTableTextBlock" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationTables" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" xlink:label="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:to="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" order="1" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShareTables" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EarningsPerShareAbstract" xlink:label="us-gaap_EarningsPerShareAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTextBlock"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNatureOfBusinessAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashCashEquivalentsAndShortTermInvestments" xlink:label="us-gaap_CashCashEquivalentsAndShortTermInvestments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedCashNoncurrent" xlink:label="us-gaap_RestrictedCashNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_CashCashEquivalentsAndShortTermInvestments" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_RestrictedCashNoncurrent" order="1" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="2" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanySClassifiedAssetsMeasuredAtFairValueOnRecurringBasisDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueDisclosuresAbstract" xlink:label="us-gaap_FairValueDisclosuresAbstract"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:label="sybx_FairValueAssetMeasuredOnRecurringBasisTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueByMeasurementFrequencyAxis" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementsRecurringMember" xlink:label="us-gaap_FairValueMeasurementsRecurringMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueInputsLevel1Member" xlink:label="us-gaap_FairValueInputsLevel1Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FinancialInstrumentAxis" xlink:label="us-gaap_FinancialInstrumentAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CorporateDebtSecuritiesMember" xlink:label="us-gaap_CorporateDebtSecuritiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentTypeAxis" xlink:label="us-gaap_InvestmentTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:label="us-gaap_InvestmentTypeCategorizationMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommercialPaperMember" xlink:label="us-gaap_CommercialPaperMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsAxis" xlink:label="us-gaap_CashAndCashEquivalentsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_MoneyMarketFundsMember" xlink:label="us-gaap_MoneyMarketFundsMember"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:label="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueInputsLevel2Member" xlink:label="us-gaap_FairValueInputsLevel2Member"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_USTreasuryAndGovernmentLongTermDebtSecuritiesMember" xlink:label="sybx_USTreasuryAndGovernmentLongTermDebtSecuritiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentsFairValueDisclosure" xlink:label="us-gaap_InvestmentsFairValueDisclosure"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueInputsLevel3Member" xlink:label="us-gaap_FairValueInputsLevel3Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AssetsFairValueDisclosure" xlink:label="us-gaap_AssetsFairValueDisclosure"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsMember" xlink:label="us-gaap_CashAndCashEquivalentsMember"/>
    <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="0" priority="2" use="optional" preferredLabel="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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="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="0" priority="2" use="optional" preferredLabel="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="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="sybx_USTreasuryAndGovernmentLongTermDebtSecuritiesMember" order="1" priority="2" use="optional" preferredLabel="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="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="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="2" priority="2" use="optional" preferredLabel="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="2" 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_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CashAndCashEquivalentsMember" order="2" priority="2" use="optional" preferredLabel="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="3" priority="2" use="optional" preferredLabel="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="4" priority="2" use="optional" preferredLabel="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="5" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestmentsSummaryOfAvailableForSaleSecuritiesHeldDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FinancialInstrumentAxis" xlink:label="us-gaap_FinancialInstrumentAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CorporateDebtSecuritiesMember" xlink:label="us-gaap_CorporateDebtSecuritiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_USGovernmentAgenciesDebtSecuritiesAndTreasuriesMember" xlink:label="sybx_USGovernmentAgenciesDebtSecuritiesAndTreasuriesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommercialPaperMember" xlink:label="us-gaap_CommercialPaperMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" order="1" priority="2" use="optional" preferredLabel="http://www.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="sybx_USGovernmentAgenciesDebtSecuritiesAndTreasuriesMember" order="1" priority="2" use="optional" preferredLabel="http://www.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_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="1" priority="2" use="optional" preferredLabel="http://www.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_CommercialPaperMember" order="2" priority="2" use="optional" preferredLabel="http://www.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="2" 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="3" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAvailableForSaleInvestmentsAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract" xlink:label="us-gaap_InvestmentsDebtAndEquitySecuritiesAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionNumberOfPositions" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPositionNumberOfPositions"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerNumberOfPositions" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleContinuousUnrealizedLossPosition12MonthsOrLongerNumberOfPositions"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleUnrealizedLossPosition"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" xlink:label="sybx_OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentAbstract" xlink:label="us-gaap_PropertyPlantAndEquipmentAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:label="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:label="us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:label="us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquipmentMember" xlink:label="us-gaap_EquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentLineItems" xlink:label="us-gaap_PropertyPlantAndEquipmentLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentGross" xlink:label="us-gaap_PropertyPlantAndEquipmentGross"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ComputerAndOfficeEquipmentMember" xlink:label="sybx_ComputerAndOfficeEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" xlink:label="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FurnitureAndFixturesMember" xlink:label="us-gaap_FurnitureAndFixturesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LeaseholdImprovementsMember" xlink:label="us-gaap_LeaseholdImprovementsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ConstructionInProgressMember" xlink:label="us-gaap_ConstructionInProgressMember"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="1" 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_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_FurnitureAndFixturesMember" order="2" priority="2" use="optional" preferredLabel="http://www.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_PropertyPlantAndEquipmentNet" order="2" 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_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_LeaseholdImprovementsMember" order="3" priority="2" use="optional" preferredLabel="http://www.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="4" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureAccruedExpensesScheduleOfAccruedExpensesDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PayablesAndAccrualsAbstract" xlink:label="us-gaap_PayablesAndAccrualsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent" xlink:label="us-gaap_EmployeeRelatedLiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccruedProfessionalFeesCurrent" xlink:label="us-gaap_AccruedProfessionalFeesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AccruedResearchAndDevelopmentCurrent" xlink:label="sybx_AccruedResearchAndDevelopmentCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherAccruedLiabilitiesCurrent" xlink:label="us-gaap_OtherAccruedLiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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="4" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquityAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityAbstract" xlink:label="us-gaap_EquityAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_GinkgoBioworksIncMember" xlink:label="sybx_GinkgoBioworksIncMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:label="us-gaap_ClassOfWarrantOrRightAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:label="us-gaap_ClassOfWarrantOrRightDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_PreFundedWarrantsMember" xlink:label="sybx_PreFundedWarrantsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AtTheMarketMember" xlink:label="sybx_AtTheMarketMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfStockLineItems" xlink:label="us-gaap_ClassOfStockLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_CowenAndCompanyLLCMember" xlink:label="sybx_CowenAndCompanyLLCMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockPricePerShare" xlink:label="us-gaap_SaleOfStockPricePerShare"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_JefferiesLLCMember" xlink:label="sybx_JefferiesLLCMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" xlink:label="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" xlink:label="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_WarrantsExercised" xlink:label="sybx_WarrantsExercised"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_ScheduleOfStockByClassTable" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="sybx_AtTheMarketMember" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_ScheduleOfStockByClassTable" xlink:to="us-gaap_ClassOfWarrantOrRightAxis" order="1" priority="2" use="optional" preferredLabel="http://www.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_CowenAndCompanyLLCMember" order="1" priority="2" use="optional" preferredLabel="http://www.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_SaleOfStockPricePerShare" order="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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_JefferiesLLCMember" order="2" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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_SubsidiarySaleOfStockAxis" order="3" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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="4" priority="2" use="optional" preferredLabel="http://www.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="4" priority="2" use="optional" preferredLabel="http://www.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="5" priority="2" use="optional" preferredLabel="http://www.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_WarrantsExercised" order="6" priority="2" use="optional" preferredLabel="http://www.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_ProceedsFromIssuanceOfCommonStock" order="7" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureStockholdersEquityScheduleOfSharesOfCommonStockReservedForFutureIssuanceDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityAbstract" xlink:label="us-gaap_EquityAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfStockByClassTable" xlink:label="us-gaap_ScheduleOfStockByClassTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:label="us-gaap_ClassOfWarrantOrRightAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:label="us-gaap_ClassOfWarrantOrRightDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_PreFundedWarrantsMember" xlink:label="sybx_PreFundedWarrantsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OptionIndexedToIssuersEquityEquityAxis" xlink:label="us-gaap_OptionIndexedToIssuersEquityEquityAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_OptionsExercisableToPurchaseCommonStockMember" xlink:label="sybx_OptionsExercisableToPurchaseCommonStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockMember" xlink:label="us-gaap_EmployeeStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfStockLineItems" xlink:label="us-gaap_ClassOfStockLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" xlink:label="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_ScheduleOfStockByClassTable" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_OptionIndexedToIssuersEquityEquityAxis" xlink:to="us-gaap_OptionIndexedToIssuersEquityTypeDomain" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:to="sybx_OptionsExercisableToPurchaseCommonStockMember" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_EmployeeStockMember" order="0" priority="2" use="optional" preferredLabel="http://www.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_CommonStockCapitalSharesReservedForFutureIssuance" order="0" priority="2" use="optional" preferredLabel="http://www.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_OptionIndexedToIssuersEquityEquityAxis" order="1" priority="2" use="optional" preferredLabel="http://www.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_SubsidiarySaleOfStockAxis" order="2" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract" xlink:label="us-gaap_DisclosureOfCompensationRelatedCostsSharebasedPaymentsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_LongTermIncentivePlan2015Member" xlink:label="sybx_LongTermIncentivePlan2015Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockMember" xlink:label="us-gaap_EmployeeStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockMember" xlink:label="us-gaap_RestrictedStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfAdditionalSharesAuthorized"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_TwoThousandSeventeenAndTwoThousandFifteenEquityIncentiveAwardPlanMember" xlink:label="sybx_TwoThousandSeventeenAndTwoThousandFifteenEquityIncentiveAwardPlanMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_EmployeeStockMember" order="0" 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_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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_TwoThousandSeventeenAndTwoThousandFifteenEquityIncentiveAwardPlanMember" order="1" priority="2" use="optional" preferredLabel="http://www.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_SubsidiarySaleOfStockAxis" order="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" order="2" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" order="3" priority="2" use="optional" preferredLabel="http://www.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="4" priority="2" use="optional" preferredLabel="http://www.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="5" priority="2" use="optional" preferredLabel="http://www.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_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" order="6" priority="2" use="optional" preferredLabel="http://www.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_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" order="7" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationScheduleOfEquityBasedCompensationExpensesDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationAxis" xlink:label="us-gaap_IncomeStatementLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_GeneralAndAdministrativeExpenseMember" xlink:label="us-gaap_GeneralAndAdministrativeExpenseMember"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureEquityBasedCompensationScheduleOfEquityBasedCompensationExpensesByAwardTypeDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockMember" xlink:label="us-gaap_EmployeeStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockMember" xlink:label="us-gaap_RestrictedStockMember"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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_SubsidiarySaleOfStockAxis" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_EmployeeStockMember" order="0" 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_AwardTypeAxis" order="1" priority="2" use="optional" preferredLabel="http://www.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="1" 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="2" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCollaborationAgreementsAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract" xlink:label="us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfArrangementAxis" xlink:label="us-gaap_TypeOfArrangementAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_RocheCollaborationAndOptionAgreementMember" xlink:label="sybx_RocheCollaborationAndOptionAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_CurrentLiabilitiesMember" xlink:label="sybx_CurrentLiabilitiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_GinkgoBioworksIncMember" xlink:label="sybx_GinkgoBioworksIncMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_Revenues" xlink:label="us-gaap_Revenues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ContractWithCustomerLiabilityCurrent" xlink:label="us-gaap_ContractWithCustomerLiabilityCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountsReceivableRelatedParties" xlink:label="us-gaap_AccountsReceivableRelatedParties"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_PrepaymentToRelatedPartyForCollaborationAgreement" xlink:label="sybx_PrepaymentToRelatedPartyForCollaborationAgreement"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" xlink:label="sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PrepaidExpenseCurrent" xlink:label="us-gaap_PrepaidExpenseCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PrepaidExpenseNoncurrent" xlink:label="us-gaap_PrepaidExpenseNoncurrent"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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_RocheCollaborationAndOptionAgreementMember" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="sybx_CurrentLiabilitiesMember" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" 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_Revenues" order="0" 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_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_BalanceSheetLocationAxis" order="1" priority="2" use="optional" preferredLabel="http://www.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_ContractWithCustomerLiabilityCurrent" order="1" 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_AccountsReceivableRelatedParties" order="2" priority="2" use="optional" preferredLabel="http://www.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_RelatedPartyTransactionsByRelatedPartyAxis" order="2" priority="2" use="optional" preferredLabel="http://www.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_PrepaymentToRelatedPartyForCollaborationAgreement" order="3" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.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_RelatedPartyTransactionCollaborationAgreementInitialTerm" order="4" priority="2" use="optional" preferredLabel="http://www.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_PrepaidExpenseCurrent" order="5" priority="2" use="optional" preferredLabel="http://www.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_PrepaidExpenseNoncurrent" order="6" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShareAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EarningsPerShareAbstract" xlink:label="us-gaap_EarningsPerShareAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightAxis" xlink:label="us-gaap_ClassOfWarrantOrRightAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightDomain" xlink:label="us-gaap_ClassOfWarrantOrRightDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_PreFundedWarrantsMember" xlink:label="sybx_PreFundedWarrantsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:label="us-gaap_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1" xlink:label="us-gaap_ClassOfWarrantOrRightExercisePriceOfWarrantsOrRights1"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" xlink:label="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label"/>
    <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="1" priority="2" use="optional" preferredLabel="http://www.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_ClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" order="1" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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="2" priority="2" use="optional" preferredLabel="http://www.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="3" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureNetLossPerShareScheduleOfPotentiallyCommonSharesExcludedFromCalculationOfNetLossPerShareDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EarningsPerShareAbstract" xlink:label="us-gaap_EarningsPerShareAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_UnvestedRestrictedStockAwardsMember" xlink:label="sybx_UnvestedRestrictedStockAwardsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockCompensationPlanMember" xlink:label="us-gaap_StockCompensationPlanMember"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_EarningsPerShareAbstract" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" order="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" order="1" priority="2" use="optional" preferredLabel="http://www.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_StockCompensationPlanMember" order="2" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:label="us-gaap_CommitmentsAndContingenciesDisclosureAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_GainContingenciesTable" xlink:label="us-gaap_GainContingenciesTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_LegalEntityAxis" xlink:label="dei_LegalEntityAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityDomain" xlink:label="dei_EntityDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AzzurGroupLimitedLiabilityCompanyMember" xlink:label="sybx_AzzurGroupLimitedLiabilityCompanyMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_GainContingenciesLineItems" xlink:label="us-gaap_GainContingenciesLineItems"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_AgreedToPayToRenovateAndUpgradeCleanroomSpace" xlink:label="sybx_AgreedToPayToRenovateAndUpgradeCleanroomSpace"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_EstimatedProjectCostForAccessPersonalSupportAndOtherServices" xlink:label="sybx_EstimatedProjectCostForAccessPersonalSupportAndOtherServices"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_CommitmentsAndContingenciesDisclosureAbstract" xlink:to="us-gaap_GainContingenciesTable" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GainContingenciesTable" xlink:to="dei_LegalEntityAxis" order="0" priority="2" use="optional" preferredLabel="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="0" priority="2" use="optional" preferredLabel="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="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GainContingenciesLineItems" xlink:to="sybx_AgreedToPayToRenovateAndUpgradeCleanroomSpace" order="0" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GainContingenciesTable" xlink:to="us-gaap_GainContingenciesLineItems" order="1" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GainContingenciesLineItems" xlink:to="sybx_EstimatedProjectCostForAccessPersonalSupportAndOtherServices" order="1" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
    <link:presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="us-gaap_GainContingenciesLineItems" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" order="2" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
  <link:presentationLink xlink:role="http://www.synlogictx.com/20220930/taxonomy/role/Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail" xlink:title="presentationLink" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsAbstract" xlink:label="us-gaap_RelatedPartyTransactionsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:label="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_GinkgoBioworksIncMember" xlink:label="sybx_GinkgoBioworksIncMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionLineItems" xlink:label="us-gaap_RelatedPartyTransactionLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockSharesOutstanding" xlink:label="us-gaap_CommonStockSharesOutstanding"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_PrepaymentToRelatedPartyForCollaborationAgreement" xlink:label="sybx_PrepaymentToRelatedPartyForCollaborationAgreement"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" xlink:label="sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_CurrentPrePaidResearchAndDevelopment" xlink:label="sybx_CurrentPrePaidResearchAndDevelopment"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_NonCurrentPrePaidResearchAndDevelopment" xlink:label="sybx_NonCurrentPrePaidResearchAndDevelopment"/>
    <link:loc xlink:type="locator" xlink:href="sybx-20220930.xsd#sybx_PrepaidResearchAndDevelopmentExpenses" xlink:label="sybx_PrepaidResearchAndDevelopmentExpenses"/>
    <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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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="0" priority="2" use="optional" preferredLabel="http://www.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_CommonStockSharesOutstanding" order="0" priority="2" use="optional" preferredLabel="http://www.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="1" priority="2" use="optional" preferredLabel="http://www.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="1" 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="sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" order="2" 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="sybx_CurrentPrePaidResearchAndDevelopment" order="3" 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="sybx_NonCurrentPrePaidResearchAndDevelopment" order="4" priority="2" use="optional" preferredLabel="http://www.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_PrepaidResearchAndDevelopmentExpenses" order="5" priority="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel"/>
  </link:presentationLink>
</link:linkbase>
