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            <funder>The present study was supported by the ANR project DECIPHER (ANR-14-CE19-0023), by the 'Chercheur d’Avenir' project TRANSGIGAS (Region Languedoc Roussillon), by the EU funded project VIVALDI (H2020 program, n°678589) and by Ifremer, CNRS, Université de Montpellier and Université de Perpignan Via Domitia. With the support of LabEx CeMEB, an ANR 'Investissements d’Avenir 'Laboratoires d'Excellences' program through the Environmental Epigenomics Platform (ANR-10-LABX-0004) and LabEx TULIP (ANR‐10‐LABX‐0041).</funder>
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                <term xml:lang="en">Oyster</term>
                <term xml:lang="en">Aquaculture</term>
                <term xml:lang="en">Microbiota</term>
                <term xml:lang="en">Innate immune shaping</term>
                <term xml:lang="en">Epigenetic</term>
                <term xml:lang="en">DNA methylation</term>
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              <p>Background: The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas , the role of the environmental microbial community on immune system maturation – and, importantly, protection from infectious disease – is still an open question.Results: Here, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific Oyster Mortality Syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS.Conclusions: We anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease.</p>
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