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    <periodOfReport>2023-06-16</periodOfReport>

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    <issuer>
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        <issuerName>Prometheus Biosciences, Inc.</issuerName>
        <issuerTradingSymbol>RXDX</issuerTradingSymbol>
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            <rptOwnerName>Marshall Keith W</rptOwnerName>
        </reportingOwnerId>
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            <rptOwnerStreet1>C/O PROMETHEUS BIOSCIENCES, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>3050 SCIENCE PARK ROAD</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
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            <officerTitle>Chief Financial Officer</officerTitle>
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    <footnotes>
        <footnote id="F1">Includes 9,811 restricted stock units.</footnote>
        <footnote id="F2">Pursuant to the Agreement and Plan of Merger, dated April 15, 2023, by and among the Issuer, Merck &amp; Co., Inc. (&quot;Merck&quot;) and Splash Merger Sub, Inc., the Issuer became a wholly owned subsidiary of Merck upon consummation of the merger (the &quot;Effective Time&quot;). At the Effective Time, (a) each of the Issuer's outstanding shares of common stock was cancelled and automatically converted into the right to receive $200 in cash (the &quot;Merger Consideration&quot;), without interest,... (Continued in Footnote 3)</footnote>
        <footnote id="F3">(Continued from Footnote 2) ...(b) each of the Issuer's outstanding restricted stock units (&quot;RSUs&quot;) was automatically cancelled and converted into the right to receive an amount in cash equal to the product of (i) the number of shares of the Issuer's common stock underlying such RSU immediately prior to the Effective Time multiplied by (ii) the Merger Consideration, without interest and (c) each of the Issuer's outstanding unexercised stock options, whether vested or unvested, was automatically cancelled and converted into the right to receive  an amount in cash, without interest, equal to the product of (i) the number of shares of the Issuer's common stock underlying such option immediately prior to the Effective Time multiplied by (ii) the amount, if any, by which the Merger Consideration exceeded the exercise price per share of such option.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Keith W. Marshall</signatureName>
        <signatureDate>2023-06-16</signatureDate>
    </ownerSignature>
</ownershipDocument>
