<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0508</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2026-03-05</periodOfReport>

    <issuer>
        <issuerCik>0001785279</issuerCik>
        <issuerName>Metagenomi Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>MGX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0002009713</rptOwnerCik>
            <rptOwnerName>Wein Matthew</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O METAGENOMI THERAPEUTICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>5959 HORTON STREET, 7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>EMERYVILLE</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94608</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>false</isDirector>
            <isOfficer>true</isOfficer>
            <isTenPercentOwner>false</isTenPercentOwner>
            <isOther>false</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <aff10b5One>false</aff10b5One>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2026-03-05</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>false</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>482</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.60</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>114549</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">These shares of common stock were automatically sold for the purpose of satisfying the Reporting Person's tax withholding obligations upon the vesting of certain restricted stock units granted to the Reporting Person on each of April 1, 2024 and April 1, 2025, and does not represent a volitional trade by the Reporting Person.</footnote>
    </footnotes>

    <remarks>Title: General Counsel, Compliance Officer and Corporate Secretary</remarks>

    <ownerSignature>
        <signatureName>/s/ Matthew L. Wein</signatureName>
        <signatureDate>2026-03-09</signatureDate>
    </ownerSignature>
</ownershipDocument>
