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Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of <jats:italic>Gammarus fossarum<\/jats:italic>, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.<\/jats:p>","DOI":"10.1038\/s41522-020-0133-2","type":"journal-article","created":{"date-parts":[[2020,6,5]],"date-time":"2020-06-05T10:04:22Z","timestamp":1591351462000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5578-3370","authenticated-orcid":false,"given":"Duarte","family":"Gouveia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Pible","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Culotta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginie","family":"Jouffret","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Geffard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaud","family":"Chaumot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davide","family":"Degli-Esposti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1589-445X","authenticated-orcid":false,"given":"Jean","family":"Armengaud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,6,5]]},"reference":[{"key":"133_CR1","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/nature11552","volume":"489","author":"V Tremaroli","year":"2012","unstructured":"Tremaroli, V. & Backhed, F. 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