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<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2021-03-25T02:55:05.4383949+00:00 -->
<!-- Version            : 5.0.1.571 -->
<!-- Package ID         : 63a33cf19a3c43e5bf5b145ef7b39a02 -->
<!-- Copyright (c) 2021 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="sybx_OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" name="OtherThanTemporaryImpairmentLossesInvestmentsNumberDebtSecuritiesAvailableForSale" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="sybx_PrepaidResearchAndDevelopmentCurrent" name="PrepaidResearchAndDevelopmentCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_AccruedResearchAndDevelopmentCurrent" name="AccruedResearchAndDevelopmentCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sybx_GinkgoBioworksIncMember" name="GinkgoBioworksIncMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_PreFundedWarrantsMember" name="PreFundedWarrantsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_AtTheMarketMember" name="AtTheMarketMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_CowenAndCompanyLLCMember" name="CowenAndCompanyLLCMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_NumberOfVotesEntitledToEachShareOfCommonStock" name="NumberOfVotesEntitledToEachShareOfCommonStock" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_SaleOfCommonStockAndPrefundedWarrantPricePerShare" name="SaleOfCommonStockAndPrefundedWarrantPricePerShare" type="num:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="sybx_ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" name="ClassOfWarrantOrRightExercisePriceOfWarrantsPaidAtClosingOfOffering" type="num:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="sybx_ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" name="ProceedsFromIssuanceOfCommonStockAndPreFundedWarrants" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_WarrantsExercised" name="WarrantsExercised" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="sybx_UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" name="UnbeneficialPercentageOfOwnershipAfterExerciseOfCommonStockOutstandingEffectToIssuance" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfSharesOutstanding" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfSharesOutstanding" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_LongTermIncentivePlan2015Member" name="LongTermIncentivePlan2015Member" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsOutstandingWeightedAverageExercisePriceAndAdditionalDisclosuresAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_EmployeesAndNonemployeesMember" name="EmployeesAndNonemployeesMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodIntrinsicValue" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodIntrinsicValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeituresAndExpirationsInPeriodIntrinsicValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_ShareBasedCompensationByShareBasedArrangementAwardOptionsAvailableForAggregateIntrinsicValue" name="ShareBasedCompensationByShareBasedArrangementAwardOptionsAvailableForAggregateIntrinsicValue" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="sybx_PrepaymentToRelatedPartyForCollaborationAgreement" name="PrepaymentToRelatedPartyForCollaborationAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sybx_RelatedPartyTransactionCollaborationAgreementInitialTerm" name="RelatedPartyTransactionCollaborationAgreementInitialTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_AbbVieAgreementMember" name="AbbVieAgreementMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_IbdcoMember" name="IbdcoMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod" name="AnticipatedCompletionOfResearchAndDevelopmentProjectsPeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_UnvestedRestrictedStockAwardsMember" name="UnvestedRestrictedStockAwardsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_IncomeTaxDisclosureLineItems" name="IncomeTaxDisclosureLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_IncomeTaxDisclosureTable" name="IncomeTaxDisclosureTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_DeferredTaxAssetsOtherLongTermLiabilities" name="DeferredTaxAssetsOtherLongTermLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_DeferredTaxAssetsLeaseLiabilities" name="DeferredTaxAssetsLeaseLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_DeferredTaxLiabilitiesRightOfUseAssets" name="DeferredTaxLiabilitiesRightOfUseAssets" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sybx_OperatingLossCarryforwardsExpirationYear" name="OperatingLossCarryforwardsExpirationYear" type="xbrli:gYearItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_OperatingLossCarryforwardsSubjectToExpiration" name="OperatingLossCarryforwardsSubjectToExpiration" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_OperatingLossCarryforwardsNotSubjectToExpiration" name="OperatingLossCarryforwardsNotSubjectToExpiration" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_RentableSpaceUnderLeaseAgreement" name="RentableSpaceUnderLeaseAgreement" type="num:areaItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_OperatingLeasesRentExpenseAnnualRentalPayments" name="OperatingLeasesRentExpenseAnnualRentalPayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_TenantImprovementInvestmentObligation" name="TenantImprovementInvestmentObligation" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="sybx_MasterContractServicesAgreementMember" name="MasterContractServicesAgreementMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_AzzurGroupLimitedLiabilityCompanyMember" name="AzzurGroupLimitedLiabilityCompanyMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_AccessAndUseOfSpaceUnderAgreement" name="AccessAndUseOfSpaceUnderAgreement" type="num:areaItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_TermOfAgreement" name="TermOfAgreement" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_AgreementExpirationDate" name="AgreementExpirationDate" type="xbrli:dateItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="sybx_EstimatedExpensesToBeIncurredInAccessAndUseOfSpaceUnderAgreement" name="EstimatedExpensesToBeIncurredInAccessAndUseOfSpaceUnderAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_OperatingAndVariableLeaseCost" name="OperatingAndVariableLeaseCost" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_OperatingLeaseCostAbstract" name="OperatingLeaseCostAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="sybx_CurrentPrePaidResearchAndDevelopment" name="CurrentPrePaidResearchAndDevelopment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_NonCurrentPrePaidResearchAndDevelopment" name="NonCurrentPrePaidResearchAndDevelopment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="sybx_PrepaidResearchAndDevelopmentExpenses" name="PrepaidResearchAndDevelopmentExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
</xsd:schema>
