<?xml version="1.0" encoding="US-ASCII"?>
<!-- DFS Xcelerate Taxonomy Definition Linkbase - http://www.dfsco.com/financial-services/ -->
<!-- Version: 6.23.6 -->
<!-- Round: 5 -->
<!-- Creation date: 2017-11-13T05:53:35Z -->
<!-- Copyright (c) 2017 Donnelley Financial, LLC. All Rights Reserved. -->
<linkbase xmlns="http://www.xbrl.org/2003/linkbase"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xmlns:xlink="http://www.w3.org/1999/xlink"
  xmlns:xbrldt="http://xbrl.org/2005/xbrldt"
  xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DocumentandEntityInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DocumentandEntityInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_StatementOfFinancialPositionClassified" roleURI="http://www.synlogictx.com/taxonomy/role/StatementOfFinancialPositionClassified"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_StatementOfFinancialPositionClassifiedParen" roleURI="http://www.synlogictx.com/taxonomy/role/StatementOfFinancialPositionClassifiedParenthetical"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_StatementOfIncome" roleURI="http://www.synlogictx.com/taxonomy/role/StatementOfIncome"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_StatementOfOtherComprehensiveIncome" roleURI="http://www.synlogictx.com/taxonomy/role/StatementOfOtherComprehensiveIncome"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_StatementOfCashFlowsIndirect" roleURI="http://www.synlogictx.com/taxonomy/role/StatementOfCashFlowsIndirect"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureNatureOfBusinessAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureNatureOfBusinessAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureMergerWithMirnaTherapeuticsAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureMergerWithMirnaTherapeuticsAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureMergerWithMirnaTherapeuticsNetAssetsAcquiredInTheMerger" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureMergerWithMirnaTherapeuticsNetAssetsAcquiredInTheMerger"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanysClassifiedAssetsMeasuredAtFairValueOnRecurringBasis" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanysClassifiedAssetsMeasuredAtFairValueOnRecurringBasis"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureAvailableforSaleSecuritiesSummaryOfAvailableforSaleSecuritiesHeld" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureAvailableforSaleSecuritiesSummaryOfAvailableforSaleSecuritiesHeld"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureAvailableforSaleSecuritiesAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureAvailableforSaleSecuritiesAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosurePrepaidExpensesAndOtherCurrentAssets" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssets"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureAccruedExpenses" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureAccruedExpenses"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureCommonStockAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureCommonStockAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosurePreferredStockAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosurePreferredStockAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureEquitybasedCompensationAndEquityIncentivePlansAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfEquitybasedCompensationExpenses" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfEquitybasedCompensationExpenses"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfEquitybasedCompensationExpensesByAwardType" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfEquitybasedCompensationExpensesByAwardType"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015LLCPlan" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015LLCPlan"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfWeightedAverageAssumptionUsedBlackScholesOptionpricingModelForAwards" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfWeightedAverageAssumptionUsedBlackScholesOptionpricingModelForAwards"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015And2017Plan" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015And2017Plan"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfRestrictedStockActivity" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfRestrictedStockActivity"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureSignificantAgreementsAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureSignificantAgreementsAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureNetLossPerShareUnitAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureNetLossPerShareUnitAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureNetLossPerShareUnitScheduleOfComputationOfBasicAndDilutedNetLossPerShare" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureNetLossPerShareUnitScheduleOfComputationOfBasicAndDilutedNetLossPerShare"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureNetLossPerShareUnitScheduleOfPotentiallyCommonSharesUnitsExcludedFromCalculationOfNetLossPerShareUnit" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureNetLossPerShareUnitScheduleOfPotentiallyCommonSharesUnitsExcludedFromCalculationOfNetLossPerShareUnit"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureCommitmentsAndContingenciesAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureRelatedPartyTransactionsAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureRelatedPartyTransactionsAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#DisclosureSubsequentEventsAdditionalInformation" roleURI="http://www.synlogictx.com/taxonomy/role/DisclosureSubsequentEventsAdditionalInformation"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsOrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsOrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsSignificantAccountingPoliciesTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsSignificantAccountingPoliciesTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsSignificantAccountingPoliciesTextBlockPolicies" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsSignificantAccountingPoliciesTextBlockPolicies"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsMergersAcquisitionsAndDispositionsDisclosuresTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsMergersAcquisitionsAndDispositionsDisclosuresTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsMergersAcquisitionsAndDispositionsDisclosuresTextBlockTables" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsMergersAcquisitionsAndDispositionsDisclosuresTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsFairValueDisclosuresTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsFairValueDisclosuresTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsFairValueDisclosuresTextBlockTables" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsFairValueDisclosuresTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsAvailableForSaleSecuritiesTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAvailableForSaleSecuritiesTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsAvailableForSaleSecuritiesTextBlockTables" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAvailableForSaleSecuritiesTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsPrepaidExpensesAndOtherCurrentAssetsTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsPrepaidExpensesAndOtherCurrentAssetsTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsPrepaidExpensesAndOtherCurrentAssetsTextBlockTables" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsPrepaidExpensesAndOtherCurrentAssetsTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsAccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsAccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlockTables" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsStockholdersEquityNoteDisclosureTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsStockholdersEquityNoteDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsPreferredStockTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsPreferredStockTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsCollaborativeArrangementDisclosureTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsCollaborativeArrangementDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsEarningsPerShareTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsEarningsPerShareTextBlockTables" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlockTables"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsCommitmentsAndContingenciesDisclosureTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsCommitmentsAndContingenciesDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock"/>
  <roleRef xlink:type="simple" xlink:href="sybx-20170930.xsd#Role_NotesToFinancialStatementsSubsequentEventsTextBlock" roleURI="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsSubsequentEventsTextBlock"/>
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all" arcroleURI="http://xbrl.org/int/dim/arcrole/all"/>
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default" arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default"/>
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain" arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain"/>
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member" arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member"/>
  <arcroleRef xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension" arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension"/>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DocumentandEntityInformation">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/StatementOfFinancialPositionClassified">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:label="us-gaap_AccountsPayableCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AdditionalPaidInCapital" xlink:label="us-gaap_AdditionalPaidInCapital"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_Assets" xlink:label="us-gaap_Assets"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AssetsAbstract" xlink:label="us-gaap_AssetsAbstract"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AssetsCurrent" xlink:label="us-gaap_AssetsCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AssetsCurrentAbstract" xlink:label="us-gaap_AssetsCurrentAbstract"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesCurrent" xlink:label="us-gaap_AvailableForSaleSecuritiesCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeaseObligationsCurrent" xlink:label="us-gaap_CapitalLeaseObligationsCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CapitalLeaseObligationsNoncurrent" xlink:label="us-gaap_CapitalLeaseObligationsNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ClassAPreferredUnitsMember" xlink:label="sybx_ClassAPreferredUnitsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ClassbPreferredUnitsMember" xlink:label="sybx_ClassbPreferredUnitsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommitmentsAndContingencies" xlink:label="us-gaap_CommitmentsAndContingencies"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonUnitIssuanceValue" xlink:label="us-gaap_CommonUnitIssuanceValue"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ContingentlyRedeemableClassaPreferredUnitsMember" xlink:label="sybx_ContingentlyRedeemableClassaPreferredUnitsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredRentCreditCurrent" xlink:label="us-gaap_DeferredRentCreditCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredRentCreditNoncurrent" xlink:label="us-gaap_DeferredRentCreditNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredRevenueCurrent" xlink:label="us-gaap_DeferredRevenueCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredRevenueNoncurrent" xlink:label="us-gaap_DeferredRevenueNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EquityAbstract" xlink:label="us-gaap_EquityAbstract"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:label="us-gaap_LiabilitiesAndStockholdersEquityAbstract"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:label="us-gaap_LiabilitiesCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesCurrentAbstract" xlink:label="us-gaap_LiabilitiesCurrentAbstract"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesNoncurrent" xlink:label="us-gaap_LiabilitiesNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LiabilitiesNoncurrentAbstract" xlink:label="us-gaap_LiabilitiesNoncurrentAbstract"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LimitedLiabilityCompanyLLCPreferredUnitIssuanceValue" xlink:label="us-gaap_LimitedLiabilityCompanyLLCPreferredUnitIssuanceValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_OtherAssetsNoncurrent" xlink:label="us-gaap_OtherAssetsNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredStockValue" xlink:label="us-gaap_PreferredStockValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredUnitsByNameAxis" xlink:label="us-gaap_PreferredUnitsByNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredUnitsClassDomain" xlink:label="us-gaap_PreferredUnitsClassDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedCashNoncurrent" xlink:label="us-gaap_RestrictedCashNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_AssetsCurrentAbstract" order="1.2800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" order="1.2900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_RestrictedCashNoncurrent" order="1.3000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_OtherAssetsNoncurrent" order="1.3100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsAbstract" xlink:to="us-gaap_Assets" order="1.3200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_AvailableForSaleSecuritiesCurrent" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AssetsCurrentAbstract" xlink:to="us-gaap_AssetsCurrent" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_PreferredStockValue" order="1.1800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_LimitedLiabilityCompanyLLCPreferredUnitIssuanceValue" order="1.1900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_CommonStockValue" order="1.2000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_CommonUnitIssuanceValue" order="1.2100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_AdditionalPaidInCapital" order="1.2200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" order="1.2300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="1.2400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityAbstract" xlink:to="us-gaap_StockholdersEquity" order="1.2500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesCurrentAbstract" order="1.3300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesNoncurrentAbstract" order="1.3400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_CommitmentsAndContingencies" order="1.3500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_EquityAbstract" order="1.3700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesAndStockholdersEquityAbstract" xlink:to="us-gaap_LiabilitiesAndStockholdersEquity" order="1.3800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccountsPayableCurrent" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_AccruedLiabilitiesCurrent" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_DeferredRevenueCurrent" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_DeferredRentCreditCurrent" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_CapitalLeaseObligationsCurrent" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesCurrentAbstract" xlink:to="us-gaap_LiabilitiesCurrent" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_DeferredRevenueNoncurrent" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_DeferredRentCreditNoncurrent" order="1.1200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_CapitalLeaseObligationsNoncurrent" order="1.1300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LiabilitiesNoncurrentAbstract" xlink:to="us-gaap_LiabilitiesNoncurrent" order="1.1400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PreferredUnitsByNameAxis" xlink:to="us-gaap_PreferredUnitsClassDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PreferredUnitsClassDomain" xlink:to="sybx_ContingentlyRedeemableClassaPreferredUnitsMember" order="1.1500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PreferredUnitsClassDomain" xlink:to="sybx_ClassbPreferredUnitsMember" order="1.1600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PreferredUnitsClassDomain" xlink:to="sybx_ClassAPreferredUnitsMember" order="1.1700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AssetsAbstract" order="1.2600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_LiabilitiesAndStockholdersEquityAbstract" order="1.2700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_PreferredUnitsByNameAxis" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/StatementOfFinancialPositionClassifiedParenthetical">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" xlink:label="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ClassAPreferredUnitsMember" xlink:label="sybx_ClassAPreferredUnitsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ClassbPreferredUnitsMember" xlink:label="sybx_ClassbPreferredUnitsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockSharesAuthorized" xlink:label="us-gaap_CommonStockSharesAuthorized"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockSharesIssued" xlink:label="us-gaap_CommonStockSharesIssued"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockSharesOutstanding" xlink:label="us-gaap_CommonStockSharesOutstanding"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonUnitIssued" xlink:label="us-gaap_CommonUnitIssued"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonUnitOutstanding" xlink:label="us-gaap_CommonUnitOutstanding"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ContingentlyRedeemableClassaPreferredUnitsMember" xlink:label="sybx_ContingentlyRedeemableClassaPreferredUnitsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LimitedLiabilityCompanyLLCPreferredUnitIssued" xlink:label="us-gaap_LimitedLiabilityCompanyLLCPreferredUnitIssued"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_LimitedLiabilityCompanyLLCPreferredUnitOutstanding" xlink:label="us-gaap_LimitedLiabilityCompanyLLCPreferredUnitOutstanding"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredStockParOrStatedValuePerShare" xlink:label="us-gaap_PreferredStockParOrStatedValuePerShare"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredStockSharesAuthorized" xlink:label="us-gaap_PreferredStockSharesAuthorized"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredStockSharesIssued" xlink:label="us-gaap_PreferredStockSharesIssued"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredStockSharesOutstanding" xlink:label="us-gaap_PreferredStockSharesOutstanding"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredUnitsByNameAxis" xlink:label="us-gaap_PreferredUnitsByNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredUnitsClassDomain" xlink:label="us-gaap_PreferredUnitsClassDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PreferredUnitsClassDomain" xlink:label="us-gaap_PreferredUnitsClassDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_PreferredUnitsByNameAxis" xlink:to="us-gaap_PreferredUnitsClassDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PreferredUnitsByNameAxis" xlink:to="us-gaap_PreferredUnitsClassDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PreferredUnitsClassDomain" xlink:to="sybx_ContingentlyRedeemableClassaPreferredUnitsMember" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PreferredUnitsClassDomain" xlink:to="sybx_ClassbPreferredUnitsMember" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PreferredUnitsClassDomain" xlink:to="sybx_ClassAPreferredUnitsMember" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_LimitedLiabilityCompanyLLCPreferredUnitIssued" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_LimitedLiabilityCompanyLLCPreferredUnitOutstanding" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_PreferredStockParOrStatedValuePerShare" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_PreferredStockSharesAuthorized" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_PreferredStockSharesIssued" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_PreferredStockSharesOutstanding" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesAuthorized" order="1.1200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesIssued" order="1.1300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesOutstanding" order="1.1400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonUnitIssued" order="1.1500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonUnitOutstanding" order="1.1600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_PreferredUnitsByNameAxis" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/StatementOfIncome">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/StatementOfOtherComprehensiveIncome">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/StatementOfCashFlowsIndirect">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureNatureOfBusinessAdditionalInformation">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CashAndCashEquivalentsLineItems" xlink:label="us-gaap_CashAndCashEquivalentsLineItems"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_CashCashEquivalentsAndMarketableSecurities" xlink:label="sybx_CashCashEquivalentsAndMarketableSecurities"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ConsolidatedEntitiesAxis" xlink:label="us-gaap_ConsolidatedEntitiesAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ConsolidatedEntitiesDomain" xlink:label="us-gaap_ConsolidatedEntitiesDomain"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MirnaTherapeuticsMember" xlink:label="sybx_MirnaTherapeuticsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_NumberOfOperatingSegments" xlink:label="us-gaap_NumberOfOperatingSegments"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ProceedsFromDivestitureOfBusinesses" xlink:label="us-gaap_ProceedsFromDivestitureOfBusinesses"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ProceedsFromIssuanceOfConvertiblePreferredStock" xlink:label="us-gaap_ProceedsFromIssuanceOfConvertiblePreferredStock"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedCashNoncurrent" xlink:label="us-gaap_RestrictedCashNoncurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfCashAndCashEquivalentsTable" xlink:label="us-gaap_ScheduleOfCashAndCashEquivalentsTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SeriesCPreferredStockMember" xlink:label="us-gaap_SeriesCPreferredStockMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StockholdersEquityNoteStockSplitConversionRatio1" xlink:label="us-gaap_StockholdersEquityNoteStockSplitConversionRatio1"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="us-gaap_ScheduleOfCashAndCashEquivalentsTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="us-gaap_StockholdersEquityNoteStockSplitConversionRatio1" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="us-gaap_NumberOfOperatingSegments" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="sybx_CashCashEquivalentsAndMarketableSecurities" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="us-gaap_RestrictedCashNoncurrent" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="us-gaap_ProceedsFromIssuanceOfConvertiblePreferredStock" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsLineItems" xlink:to="us-gaap_ProceedsFromDivestitureOfBusinesses" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="us-gaap_SeriesCPreferredStockMember" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_ConsolidatedEntitiesAxis" xlink:to="us-gaap_ConsolidatedEntitiesDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ConsolidatedEntitiesDomain" xlink:to="sybx_MirnaTherapeuticsMember" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCashAndCashEquivalentsTable" xlink:to="us-gaap_ConsolidatedEntitiesAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCashAndCashEquivalentsTable" xlink:to="us-gaap_StatementClassOfStockAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformation">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureMergerWithMirnaTherapeuticsAdditionalInformation">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionAcquireeDomain" xlink:label="us-gaap_BusinessAcquisitionAcquireeDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionAcquireeDomain" xlink:label="us-gaap_BusinessAcquisitionAcquireeDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionAxis" xlink:label="us-gaap_BusinessAcquisitionAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionLineItems" xlink:label="us-gaap_BusinessAcquisitionLineItems"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_CommonStockExchangeRatio" xlink:label="sybx_CommonStockExchangeRatio"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockSharesOutstanding" xlink:label="us-gaap_CommonStockSharesOutstanding"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ConsolidatedEntitiesAxis" xlink:label="us-gaap_ConsolidatedEntitiesAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ConsolidatedEntitiesDomain" xlink:label="us-gaap_ConsolidatedEntitiesDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ConsolidatedEntitiesDomain" xlink:label="us-gaap_ConsolidatedEntitiesDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2014/dei-2014-01-31.xsd#dei_EntityDomain" xlink:label="dei_EntityDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2014/dei-2014-01-31.xsd#dei_EntityDomain" xlink:label="dei_EntityDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueNetAssetLiability" xlink:label="us-gaap_FairValueNetAssetLiability"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.sec.gov/dei/2014/dei-2014-01-31.xsd#dei_LegalEntityAxis" xlink:label="dei_LegalEntityAxis"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MarketCapitalization" xlink:label="sybx_MarketCapitalization"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MergerAgreementMember" xlink:label="sybx_MergerAgreementMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MirnaTherapeuticsMember" xlink:label="sybx_MirnaTherapeuticsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_NumberOfMembersOnBoardOfDirectors" xlink:label="sybx_NumberOfMembersOnBoardOfDirectors"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_PercentageOfFullyDilutedCommonStockIssuedAsOptions" xlink:label="sybx_PercentageOfFullyDilutedCommonStockIssuedAsOptions"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:label="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsidiaryOrEquityMethodInvesteeCumulativePercentageOwnershipAfterAllTransactions" xlink:label="us-gaap_SubsidiaryOrEquityMethodInvesteeCumulativePercentageOwnershipAfterAllTransactions"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_SynlogicMember" xlink:label="sybx_SynlogicMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionAcquireeDomain" xlink:to="sybx_MergerAgreementMember" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_BusinessAcquisitionAxis" xlink:to="us-gaap_BusinessAcquisitionAcquireeDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BusinessAcquisitionAxis" xlink:to="us-gaap_BusinessAcquisitionAcquireeDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_SubsidiaryOrEquityMethodInvesteeCumulativePercentageOwnershipAfterAllTransactions" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="sybx_NumberOfMembersOnBoardOfDirectors" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="sybx_CommonStockExchangeRatio" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_CommonStockSharesOutstanding" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="sybx_PercentageOfFullyDilutedCommonStockIssuedAsOptions" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="sybx_MarketCapitalization" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_FairValueNetAssetLiability" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_ConsolidatedEntitiesAxis" xlink:to="us-gaap_ConsolidatedEntitiesDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_ConsolidatedEntitiesAxis" xlink:to="us-gaap_ConsolidatedEntitiesDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ConsolidatedEntitiesDomain" xlink:to="sybx_MirnaTherapeuticsMember" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="dei_EntityDomain" xlink:to="sybx_SynlogicMember" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="dei_LegalEntityAxis" xlink:to="dei_EntityDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_BusinessAcquisitionAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="dei_LegalEntityAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_ConsolidatedEntitiesAxis" order="4.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureMergerWithMirnaTherapeuticsNetAssetsAcquiredInTheMerger">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionAcquireeDomain" xlink:label="us-gaap_BusinessAcquisitionAcquireeDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionAxis" xlink:label="us-gaap_BusinessAcquisitionAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionCostOfAcquiredEntityTransactionCosts" xlink:label="us-gaap_BusinessAcquisitionCostOfAcquiredEntityTransactionCosts"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionLineItems" xlink:label="us-gaap_BusinessAcquisitionLineItems"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedAccumulatedOtherComprehensiveIncome" xlink:label="sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedAccumulatedOtherComprehensiveIncome"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCashAndEquivalents" xlink:label="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCashAndEquivalents"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsMarketableSecurities" xlink:label="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsMarketableSecurities"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsPrepaidExpenseAndOtherAssets" xlink:label="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsPrepaidExpenseAndOtherAssets"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsReceivables" xlink:label="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsReceivables"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentLiabilitiesAccountsPayableAndAccruedExpenses" xlink:label="sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentLiabilitiesAccountsPayableAndAccruedExpenses"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedNet" xlink:label="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedNet"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedNetLessTransactionCosts" xlink:label="sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedNetLessTransactionCosts"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MirnaTherapeuticsMember" xlink:label="sybx_MirnaTherapeuticsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:label="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionAcquireeDomain" xlink:to="sybx_MirnaTherapeuticsMember" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BusinessAcquisitionAxis" xlink:to="us-gaap_BusinessAcquisitionAcquireeDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCashAndEquivalents" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsMarketableSecurities" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsReceivables" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentAssetsPrepaidExpenseAndOtherAssets" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedAccumulatedOtherComprehensiveIncome" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedCurrentLiabilitiesAccountsPayableAndAccruedExpenses" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedNet" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="us-gaap_BusinessAcquisitionCostOfAcquiredEntityTransactionCosts" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionLineItems" xlink:to="sybx_BusinessCombinationRecognizedIdentifiableAssetsAcquiredAndLiabilitiesAssumedNetLessTransactionCosts" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_BusinessAcquisitionAxis" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureFairValueOfFinancialInstrumentsScheduleOfCompanysClassifiedAssetsMeasuredAtFairValueOnRecurringBasis">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AssetsFairValueDisclosure" xlink:label="us-gaap_AssetsFairValueDisclosure"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesCurrent" xlink:label="us-gaap_AvailableForSaleSecuritiesCurrent"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CashAndCashEquivalentsAxis" xlink:label="us-gaap_CashAndCashEquivalentsAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:label="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:label="sybx_FairValueAssetMeasuredOnRecurringBasisTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueByMeasurementFrequencyAxis" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueInputsLevel1Member" xlink:label="us-gaap_FairValueInputsLevel1Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueInputsLevel2Member" xlink:label="us-gaap_FairValueInputsLevel2Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueInputsLevel3Member" xlink:label="us-gaap_FairValueInputsLevel3Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FairValueMeasurementsRecurringMember" xlink:label="us-gaap_FairValueMeasurementsRecurringMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MoneyMarketFundsMember" xlink:label="us-gaap_MoneyMarketFundsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_USGovernmentSponsoredEnterprisesDebtSecuritiesMember" xlink:label="us-gaap_USGovernmentSponsoredEnterprisesDebtSecuritiesMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_USTreasurySecuritiesMember" xlink:label="us-gaap_USTreasurySecuritiesMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_CashAndCashEquivalentsAxis" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_CashAndCashEquivalentsAxis" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="sybx_FairValueAssetMeasuredOnRecurringBasisTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesCurrent" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisLineItems" xlink:to="us-gaap_AssetsFairValueDisclosure" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_FairValueByMeasurementFrequencyAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_CashAndCashEquivalentsAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="sybx_FairValueAssetMeasuredOnRecurringBasisTable" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" order="4.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementFrequencyDomain" xlink:to="us-gaap_FairValueMeasurementsRecurringMember" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel1Member" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel2Member" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel3Member" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:to="us-gaap_USGovernmentSponsoredEnterprisesDebtSecuritiesMember" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:to="us-gaap_USTreasurySecuritiesMember" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:to="us-gaap_MoneyMarketFundsMember" order="1.0400" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureAvailableforSaleSecuritiesSummaryOfAvailableforSaleSecuritiesHeld">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecurities" xlink:label="us-gaap_AvailableForSaleSecurities"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:label="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:label="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:label="us-gaap_AvailableForSaleSecuritiesAmortizedCost"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:label="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesTable" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_USGovernmentSponsoredEnterprisesDebtSecuritiesMember" xlink:label="us-gaap_USGovernmentSponsoredEnterprisesDebtSecuritiesMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_USTreasurySecuritiesMember" xlink:label="us-gaap_USTreasurySecuritiesMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:to="us-gaap_USGovernmentSponsoredEnterprisesDebtSecuritiesMember" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_MajorTypesOfDebtAndEquitySecuritiesDomain" xlink:to="us-gaap_USTreasurySecuritiesMember" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_ScheduleOfAvailableForSaleSecuritiesTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesAmortizedCost" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecurities" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesTable" xlink:to="us-gaap_MajorTypesOfDebtAndEquitySecuritiesAxis" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureAvailableforSaleSecuritiesAdditionalInformation">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosurePrepaidExpensesAndOtherCurrentAssets">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureAccruedExpenses">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureCommonStockAdditionalInformation">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosurePreferredStockAdditionalInformation">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansAdditionalInformation">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain_2"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_CommonStockExchangeRatio" xlink:label="sybx_CommonStockExchangeRatio"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_CommonUnitsMember" xlink:label="sybx_CommonUnitsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_EmployeeMember" xlink:label="sybx_EmployeeMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_EmployeesAndConsultantsMember" xlink:label="sybx_EmployeesAndConsultantsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain_2"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2015And2017Member" xlink:label="sybx_LongTermIncentivePlan2015And2017Member"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2015Member" xlink:label="sybx_LongTermIncentivePlan2015Member"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_NonemployeeMember" xlink:label="sybx_NonemployeeMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PhantomShareUnitsPSUsMember" xlink:label="us-gaap_PhantomShareUnitsPSUsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedStockMember" xlink:label="us-gaap_RestrictedStockMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedStockUnitsRSUMember" xlink:label="us-gaap_RestrictedStockUnitsRSUMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanAxis" xlink:label="us-gaap_RestructuringPlanAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanDomain" xlink:label="us-gaap_RestructuringPlanDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanDomain" xlink:label="us-gaap_RestructuringPlanDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedAtGrantDate" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedAtGrantDate"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodAggregateGrantDateFairValue" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodAggregateGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOtherThanOptionsVestedAndExpectedToVestOutstandingNumber" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOtherThanOptionsVestedAndExpectedToVestOutstandingNumber"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesIssuedInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesIssuedInPeriod"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TitleOfIndividualAxis" xlink:label="us-gaap_TitleOfIndividualAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:label="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:label="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain_2"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_TwoThousandSeventeenReorganizationMember" xlink:label="sybx_TwoThousandSeventeenReorganizationMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="sybx_CommonUnitsMember" order="1.1900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="1.2200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015And2017Member" order="1.1800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015Member" order="1.2400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RestructuringPlanAxis" xlink:to="us-gaap_RestructuringPlanDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RestructuringPlanAxis" xlink:to="us-gaap_RestructuringPlanDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringPlanDomain" xlink:to="sybx_TwoThousandSeventeenReorganizationMember" order="1.2300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_RestructuringPlanAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_StatementClassOfStockAxis" order="4.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_TitleOfIndividualAxis" order="5.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="6.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensation" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardSharesIssuedInPeriod" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedStockOptions" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedShareBasedAwardsOtherThanOptions" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_CommonStockExchangeRatio" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodAggregateGrantDateFairValue" order="1.1200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" order="1.1300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeServiceShareBasedCompensationNonvestedAwardsTotalCompensationCostNotYetRecognizedPeriodForRecognition1" order="1.1400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" order="1.1500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedAtGrantDate" order="1.1600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOtherThanOptionsVestedAndExpectedToVestOutstandingNumber" order="1.1700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockMember" order="1.2100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_PhantomShareUnitsPSUsMember" order="1.2500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" order="1.2700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_TitleOfIndividualAxis" xlink:to="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TitleOfIndividualAxis" xlink:to="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="sybx_EmployeesAndConsultantsMember" order="1.2000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="sybx_EmployeeMember" order="1.2600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="sybx_NonemployeeMember" order="1.2800" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfEquitybasedCompensationExpenses">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_GeneralAndAdministrativeExpenseMember" xlink:label="us-gaap_GeneralAndAdministrativeExpenseMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncomeStatementLocationAxis" xlink:label="us-gaap_IncomeStatementLocationAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_GeneralAndAdministrativeExpenseMember" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_IncomeStatementLocationAxis" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfEquitybasedCompensationExpensesByAwardType">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_CommonUnitsMember" xlink:label="sybx_CommonUnitsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PhantomShareUnitsPSUsMember" xlink:label="us-gaap_PhantomShareUnitsPSUsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedStockMember" xlink:label="us-gaap_RestrictedStockMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedStockUnitsRSUMember" xlink:label="us-gaap_RestrictedStockUnitsRSUMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="us-gaap_CommonStockMember" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="sybx_CommonUnitsMember" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_StatementClassOfStockAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensation" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockMember" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_PhantomShareUnitsPSUsMember" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015LLCPlan">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2015Member" xlink:label="sybx_LongTermIncentivePlan2015Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MaximumMember" xlink:label="us-gaap_MaximumMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PhantomShareUnitsPSUsMember" xlink:label="us-gaap_PhantomShareUnitsPSUsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RangeAxis" xlink:label="us-gaap_RangeAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RangeMember" xlink:label="us-gaap_RangeMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RangeMember" xlink:label="us-gaap_RangeMember_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanAxis" xlink:label="us-gaap_RestructuringPlanAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanDomain" xlink:label="us-gaap_RestructuringPlanDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedNumberOfShares" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedNumberOfShares"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsNonvestedOptionsCancelledNumberOfShares" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsNonvestedOptionsCancelledNumberOfShares"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsNonvestedOptionsCancelledWeightedAverageGrantDateFairValue" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsNonvestedOptionsCancelledWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedNumberOfShares" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedNumberOfShares"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedWeightedAverageGrantDateFairValue" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedWeightedAverageGrantDateFairValue" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageGrantDateFairValue" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedNumberOfShares" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedNumberOfShares"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedWeightedAverageGrantDateFairValue" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsCancelledInPeriodWeightedAverageExercisePrice" xlink:label="sybx_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsCancelledInPeriodWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsVestedInPeriodWeightedAverageExercisePrice" xlink:label="sybx_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsVestedInPeriodWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_TwoThousandSeventeenReorganizationMember" xlink:label="sybx_TwoThousandSeventeenReorganizationMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015Member" order="1.2300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RangeAxis" xlink:to="us-gaap_RangeMember" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RangeAxis" xlink:to="us-gaap_RangeMember_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RangeMember" xlink:to="us-gaap_MaximumMember" order="1.2500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RestructuringPlanAxis" xlink:to="us-gaap_RestructuringPlanDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringPlanDomain" xlink:to="sybx_TwoThousandSeventeenReorganizationMember" order="1.2400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_RestructuringPlanAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_RangeAxis" order="4.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedNumberOfShares" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedNumberOfShares" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedNumberOfShares" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsNonvestedOptionsCancelledNumberOfShares" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsVestedInPeriodWeightedAverageExercisePrice" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsCancelledInPeriodWeightedAverageExercisePrice" order="1.1200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice" order="1.1400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedWeightedAverageGrantDateFairValue" order="1.1500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" order="1.1600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedWeightedAverageGrantDateFairValue" order="1.1700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsNonvestedOptionsForfeitedWeightedAverageGrantDateFairValue" order="1.1800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsNonvestedOptionsCancelledWeightedAverageGrantDateFairValue" order="1.1900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageGrantDateFairValue" order="1.2100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_PhantomShareUnitsPSUsMember" order="1.2200" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfWeightedAverageAssumptionUsedBlackScholesOptionpricingModelForAwards">
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_EmployeeMember" xlink:label="sybx_EmployeeMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2015And2017Member" xlink:label="sybx_LongTermIncentivePlan2015And2017Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MaximumMember" xlink:label="us-gaap_MaximumMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_MinimumMember" xlink:label="us-gaap_MinimumMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_NonemployeeMember" xlink:label="sybx_NonemployeeMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RangeAxis" xlink:label="us-gaap_RangeAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RangeMember" xlink:label="us-gaap_RangeMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TitleOfIndividualAxis" xlink:label="us-gaap_TitleOfIndividualAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:label="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015And2017Member" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RangeAxis" xlink:to="us-gaap_RangeMember" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RangeMember" xlink:to="us-gaap_MinimumMember" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RangeMember" xlink:to="us-gaap_MaximumMember" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_RangeAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_TitleOfIndividualAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TitleOfIndividualAxis" xlink:to="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="sybx_EmployeeMember" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="sybx_NonemployeeMember" order="1.0200" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfStockOptionActivityUnder2015And2017Plan">
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2015And2017Member" xlink:label="sybx_LongTermIncentivePlan2015And2017Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanAxis" xlink:label="us-gaap_RestructuringPlanAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanDomain" xlink:label="us-gaap_RestructuringPlanDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodWeightedAverageRemainingContractualTerm" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodWeightedAverageRemainingContractualTerm"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresInPeriod"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedInPeriodIntrinsicValue" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedInPeriodIntrinsicValue"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedIntrinsicValue" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedIntrinsicValue"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedWeightedAverageRemainingContractualTerm" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedWeightedAverageRemainingContractualTerm"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedWeightedAverageRemainingContractualTerm2" xlink:label="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedWeightedAverageRemainingContractualTerm2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_TwoThousandSeventeenReorganizationMember" xlink:label="sybx_TwoThousandSeventeenReorganizationMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015And2017Member" order="1.2700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RestructuringPlanAxis" xlink:to="us-gaap_RestructuringPlanDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringPlanDomain" xlink:to="sybx_TwoThousandSeventeenReorganizationMember" order="1.2800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_RestructuringPlanAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingNumber" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresInPeriod" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingNumber" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableNumber" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePrice" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageExercisePrice" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsExercisesInPeriodWeightedAverageExercisePrice" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsForfeituresInPeriodWeightedAverageExercisePrice" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageExercisePrice" order="1.1300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisableWeightedAverageExercisePrice" order="1.1400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedWeightedAverageRemainingContractualTerm2" order="1.1500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedWeightedAverageRemainingContractualTerm" order="1.1600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodWeightedAverageRemainingContractualTerm" order="1.1700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingWeightedAverageRemainingContractualTerm1" order="1.1800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableWeightedAverageRemainingContractualTerm1" order="1.1900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingIntrinsicValue" order="1.2000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedIntrinsicValue" order="1.2100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantedInPeriodIntrinsicValue" order="1.2200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue" order="1.2300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestOutstandingAggregateIntrinsicValue" order="1.2500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardOptionsExercisableIntrinsicValue1" order="1.2600" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureEquitybasedCompensationAndEquityIncentivePlansScheduleOfRestrictedStockActivity">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2017Member" xlink:label="sybx_LongTermIncentivePlan2017Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestrictedStockMember" xlink:label="us-gaap_RestrictedStockMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanAxis" xlink:label="us-gaap_RestructuringPlanAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringPlanDomain" xlink:label="us-gaap_RestructuringPlanDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_TwoThousandSeventeenReorganizationMember" xlink:label="sybx_TwoThousandSeventeenReorganizationMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2017Member" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RestructuringPlanAxis" xlink:to="us-gaap_RestructuringPlanDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringPlanDomain" xlink:to="sybx_TwoThousandSeventeenReorganizationMember" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockMember" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue" order="1.1200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue" order="1.1300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_AwardTypeAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_PlanNameAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_RestructuringPlanAxis" order="4.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureSignificantAgreementsAdditionalInformation">
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_AbbVieMember" xlink:label="sybx_AbbVieMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AccruedLiabilitiesCurrentAndNoncurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrentAndNoncurrent"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_AcquisitionDateLineItems" xlink:label="sybx_AcquisitionDateLineItems"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod" xlink:label="sybx_AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionAcquireeDomain" xlink:label="us-gaap_BusinessAcquisitionAcquireeDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_BusinessAcquisitionAxis" xlink:label="us-gaap_BusinessAcquisitionAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ClassOfStockDomain" xlink:label="us-gaap_ClassOfStockDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_CommonUnitsMember" xlink:label="sybx_CommonUnitsMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CostOfServicesLicensesAndServices" xlink:label="us-gaap_CostOfServicesLicensesAndServices"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DeferredRevenue" xlink:label="us-gaap_DeferredRevenue"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FinitelivedIntangibleAssetsAcquired1" xlink:label="us-gaap_FinitelivedIntangibleAssetsAcquired1"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FiniteLivedIntangibleAssetsByMajorClassAxis" xlink:label="us-gaap_FiniteLivedIntangibleAssetsByMajorClassAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain" xlink:label="us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain" xlink:label="us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain_2"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_IbdcoMember" xlink:label="sybx_IbdcoMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_IntellectualPropertyMember" xlink:label="us-gaap_IntellectualPropertyMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MassachusettsInstituteOfTechnologyAndBostonUniversityLicenseAgreementMember" xlink:label="sybx_MassachusettsInstituteOfTechnologyAndBostonUniversityLicenseAgreementMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MilestonePayments" xlink:label="sybx_MilestonePayments"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_MirnaTherapeuticsMember" xlink:label="sybx_MirnaTherapeuticsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_NumberOfResearchAndDevelopmentMilestone" xlink:label="sybx_NumberOfResearchAndDevelopmentMilestone"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PatentsMember" xlink:label="us-gaap_PatentsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_PotentialMilestonePayment" xlink:label="sybx_PotentialMilestonePayment"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RestructuringCostAndReserveAxis" xlink:label="us-gaap_RestructuringCostAndReserveAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_Revenues" xlink:label="us-gaap_Revenues"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:label="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementClassOfStockAxis" xlink:label="us-gaap_StatementClassOfStockAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesConversionOfUnits" xlink:label="us-gaap_StockIssuedDuringPeriodSharesConversionOfUnits"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StockIssuedDuringPeriodSharesPurchaseOfAssets" xlink:label="us-gaap_StockIssuedDuringPeriodSharesPurchaseOfAssets"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_TwoThousandSeventeenReorganizationMember" xlink:label="sybx_TwoThousandSeventeenReorganizationMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TypeOfArrangementAxis" xlink:label="us-gaap_TypeOfArrangementAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TypeOfRestructuringDomain" xlink:label="us-gaap_TypeOfRestructuringDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TypeOfRestructuringDomain" xlink:label="us-gaap_TypeOfRestructuringDomain_2"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_UpfrontPayments" xlink:label="sybx_UpfrontPayments"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="sybx_UpfrontPayments" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="sybx_PotentialMilestonePayment" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="sybx_MilestonePayments" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="sybx_NumberOfResearchAndDevelopmentMilestone" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="sybx_AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_Revenues" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_DeferredRevenue" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_FinitelivedIntangibleAssetsAcquired1" order="1.0800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesPurchaseOfAssets" order="1.0900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesConversionOfUnits" order="1.1000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_CostOfServicesLicensesAndServices" order="1.1100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_AcquisitionDateLineItems" xlink:to="us-gaap_AccruedLiabilitiesCurrentAndNoncurrent" order="1.1200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sybx_AbbVieMember" order="1.1400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sybx_MassachusettsInstituteOfTechnologyAndBostonUniversityLicenseAgreementMember" order="1.2100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionAcquireeDomain" xlink:to="sybx_IbdcoMember" order="1.1300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BusinessAcquisitionAcquireeDomain" xlink:to="sybx_MirnaTherapeuticsMember" order="1.1900" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BusinessAcquisitionAxis" xlink:to="us-gaap_BusinessAcquisitionAcquireeDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ClassOfStockDomain" xlink:to="sybx_CommonUnitsMember" order="1.1600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" order="1.1800" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FiniteLivedIntangibleAssetsByMajorClassAxis" xlink:to="us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FiniteLivedIntangibleAssetsByMajorClassAxis" xlink:to="us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain" xlink:to="us-gaap_IntellectualPropertyMember" order="1.1500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FiniteLivedIntangibleAssetsMajorClassNameDomain" xlink:to="us-gaap_PatentsMember" order="1.2000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RestructuringCostAndReserveAxis" xlink:to="us-gaap_TypeOfRestructuringDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RestructuringCostAndReserveAxis" xlink:to="us-gaap_TypeOfRestructuringDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_FiniteLivedIntangibleAssetsByMajorClassAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_BusinessAcquisitionAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_StatementEquityComponentsAxis" order="4.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_StatementClassOfStockAxis" order="5.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfBusinessAcquisitionsByAcquisitionTable" xlink:to="us-gaap_RestructuringCostAndReserveAxis" order="6.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementClassOfStockAxis" xlink:to="us-gaap_ClassOfStockDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfRestructuringDomain" xlink:to="sybx_TwoThousandSeventeenReorganizationMember" order="1.1700" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureNetLossPerShareUnitAdditionalInformation">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureNetLossPerShareUnitScheduleOfComputationOfBasicAndDilutedNetLossPerShare">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureNetLossPerShareUnitScheduleOfPotentiallyCommonSharesUnitsExcludedFromCalculationOfNetLossPerShareUnit">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_UnvestedRestrictedStockAwardsMember" xlink:label="sybx_UnvestedRestrictedStockAwardsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_UnvestedRestrictedStockUnitsMember" xlink:label="sybx_UnvestedRestrictedStockUnitsMember"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="sybx_UnvestedRestrictedStockUnitsMember" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="sybx_UnvestedRestrictedStockAwardsMember" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureCommitmentsAndContingenciesAdditionalInformation">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureRelatedPartyTransactionsAdditionalInformation">
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_AccruedInterestRateOfLoan" xlink:label="sybx_AccruedInterestRateOfLoan"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ChiefExecutiveOfficerMember" xlink:label="us-gaap_ChiefExecutiveOfficerMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ChiefMedicalOfficerMember" xlink:label="sybx_ChiefMedicalOfficerMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ChiefOperatingOfficerMember" xlink:label="us-gaap_ChiefOperatingOfficerMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_PaymentsToRelatedParty" xlink:label="sybx_PaymentsToRelatedParty"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ProceedsFromRepaymentsOfDebt" xlink:label="us-gaap_ProceedsFromRepaymentsOfDebt"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_RelatedPartyTransactionsReimbursementsToRelatedParty" xlink:label="sybx_RelatedPartyTransactionsReimbursementsToRelatedParty"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_ScheduleOfOtherRelatedPartyTransactionsLineItems" xlink:label="sybx_ScheduleOfOtherRelatedPartyTransactionsLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:label="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TitleOfIndividualAxis" xlink:label="us-gaap_TitleOfIndividualAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:label="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="us-gaap_ChiefExecutiveOfficerMember" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="sybx_ChiefMedicalOfficerMember" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="sybx_ScheduleOfOtherRelatedPartyTransactionsLineItems" xlink:to="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_ScheduleOfOtherRelatedPartyTransactionsLineItems" xlink:to="us-gaap_ProceedsFromRepaymentsOfDebt" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_ScheduleOfOtherRelatedPartyTransactionsLineItems" xlink:to="sybx_AccruedInterestRateOfLoan" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_ScheduleOfOtherRelatedPartyTransactionsLineItems" xlink:to="sybx_PaymentsToRelatedParty" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="sybx_ScheduleOfOtherRelatedPartyTransactionsLineItems" xlink:to="sybx_RelatedPartyTransactionsReimbursementsToRelatedParty" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_TitleOfIndividualAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TitleOfIndividualAxis" xlink:to="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="us-gaap_ChiefOperatingOfficerMember" order="1.0600" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/DisclosureSubsequentEventsAdditionalInformation">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_AtTheMarketProgramMember" xlink:label="sybx_AtTheMarketProgramMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_CounterpartyNameAxis" xlink:label="us-gaap_CounterpartyNameAxis"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_CowenAndCompanyLLCMember" xlink:label="sybx_CowenAndCompanyLLCMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RepurchaseAgreementCounterpartyNameDomain" xlink:label="us-gaap_RepurchaseAgreementCounterpartyNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_RepurchaseAgreementCounterpartyNameDomain" xlink:label="us-gaap_RepurchaseAgreementCounterpartyNameDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain_2"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_SalesAgreementMember" xlink:label="sybx_SalesAgreementMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsequentEventLineItems" xlink:label="us-gaap_SubsequentEventLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsequentEventMember" xlink:label="us-gaap_SubsequentEventMember"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsequentEventTable" xlink:label="us-gaap_SubsequentEventTable"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsequentEventTypeAxis" xlink:label="us-gaap_SubsequentEventTypeAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsequentEventTypeDomain" xlink:label="us-gaap_SubsequentEventTypeDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsequentEventTypeDomain" xlink:label="us-gaap_SubsequentEventTypeDomain_2"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_TypeOfArrangementAxis" xlink:label="us-gaap_TypeOfArrangementAxis"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="sybx_SalesAgreementMember" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_CounterpartyNameAxis" xlink:to="us-gaap_RepurchaseAgreementCounterpartyNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_CounterpartyNameAxis" xlink:to="us-gaap_RepurchaseAgreementCounterpartyNameDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RepurchaseAgreementCounterpartyNameDomain" xlink:to="sybx_CowenAndCompanyLLCMember" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="sybx_AtTheMarketProgramMember" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_SubsequentEventLineItems" xlink:to="us-gaap_SubsequentEventTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SubsequentEventLineItems" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_SubsequentEventTable" xlink:to="us-gaap_SubsequentEventTypeAxis" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_SubsequentEventTable" xlink:to="us-gaap_TypeOfArrangementAxis" order="2.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_SubsequentEventTable" xlink:to="us-gaap_CounterpartyNameAxis" order="3.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_SubsequentEventTable" xlink:to="us-gaap_SubsidiarySaleOfStockAxis" order="4.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_SubsequentEventTypeAxis" xlink:to="us-gaap_SubsequentEventTypeDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsequentEventTypeAxis" xlink:to="us-gaap_SubsequentEventTypeDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SubsequentEventTypeDomain" xlink:to="us-gaap_SubsequentEventMember" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain_2" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsOrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsSignificantAccountingPoliciesTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsSignificantAccountingPoliciesTextBlockPolicies">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsMergersAcquisitionsAndDispositionsDisclosuresTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsMergersAcquisitionsAndDispositionsDisclosuresTextBlockTables">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsFairValueDisclosuresTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsFairValueDisclosuresTextBlockTables">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAvailableForSaleSecuritiesTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAvailableForSaleSecuritiesTextBlockTables">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsPrepaidExpensesAndOtherCurrentAssetsTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsPrepaidExpensesAndOtherCurrentAssetsTextBlockTables">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsAccountsPayableAccruedLiabilitiesAndOtherLiabilitiesDisclosureCurrentTextBlockTables">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsStockholdersEquityNoteDisclosureTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsPreferredStockTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsDisclosureOfCompensationRelatedCostsShareBasedPaymentsTextBlockTables">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" xlink:label="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2015And2017Member" xlink:label="sybx_LongTermIncentivePlan2015And2017Member"/>
    <loc xlink:type="locator" xlink:href="sybx-20170930.xsd#sybx_LongTermIncentivePlan2015Member" xlink:label="sybx_LongTermIncentivePlan2015Member"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationRestrictedStockUnitsAwardActivityTableTextBlock" xlink:label="us-gaap_ScheduleOfShareBasedCompensationRestrictedStockUnitsAwardActivityTableTextBlock"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedCompensationStockOptionsActivityTableTextBlock" xlink:label="us-gaap_ScheduleOfShareBasedCompensationStockOptionsActivityTableTextBlock"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock" xlink:label="us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2017/elts/us-gaap-2017-01-31.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" order="1.0000" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015Member" order="1.0100" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="sybx_LongTermIncentivePlan2015And2017Member" order="1.0200" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" order="100.0000" xbrldt:closed="true" xbrldt:contextElement="segment" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" order="1.0300" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" order="1.0400" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationStockOptionsActivityTableTextBlock" order="1.0500" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock" order="1.0600" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationRestrictedStockUnitsAwardActivityTableTextBlock" order="1.0700" priority="2" use="optional"/>
    <definitionArc xlink:type="arc" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_PlanNameAxis" order="1.0000" priority="2" use="optional"/>
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsCollaborativeArrangementDisclosureTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsEarningsPerShareTextBlockTables">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsCommitmentsAndContingenciesDisclosureTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsRelatedPartyTransactionsDisclosureTextBlock">
  </definitionLink>
  <definitionLink xlink:type="extended" xlink:role="http://www.synlogictx.com/taxonomy/role/NotesToFinancialStatementsSubsequentEventsTextBlock">
  </definitionLink>
</linkbase>
