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In it, food is chemically broken down and bacterial load reduced by gastric acid in the stomach, acting as a \u201cgatekeeper\u201d for microbes entering the intestines where chyme nutrients and water are absorbed. The natural microbiota across gastrointestinal tract zones support digestion, compete with ingested pathogens and acts itself as an immune stimulus. Despite its important role, several lineages of fish, such as pipefishes, have secondarily lost their stomach and evolved agastric digestion, with unknown consequences to their intestines\u2019 microbiomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here, we test how stomach loss might affect the microbiome by investigating the fore-, mid- and hindgut\u2019s autochthonous microbiota of the Baltic Sea broadnosed pipefish,\n                      <jats:italic>Syngnathus typhle<\/jats:italic>\n                      , and comparing it to the stomach, fore- and hindgut\u2019s autochthonous microbiota of the sympatric and ecologically similar three-spine stickleback,\n                      <jats:italic>Gasterosteus aculeatus<\/jats:italic>\n                      . Using 16S-rRNA gene sequencing and qPCR, we show that microbial abundance is high in the stomach, accompanied by high alpha diversity, but low in the intestine of\n                      <jats:italic>G. aculeatus<\/jats:italic>\n                      , although microbial diversity remains at intermediate levels \u2013 a pattern almost inversed in\n                      <jats:italic>S. typhle<\/jats:italic>\n                      .\n                      <jats:italic>G. aculeatus<\/jats:italic>\n                      \u2019 stomach has the most distinct microbiota across gastrointestinal zones; however, this species\u2019 intestines\u2019 microbes are also found in\n                      <jats:italic>S. typhle<\/jats:italic>\n                      . In contrast, the pipefish\u2019s hindgut is the most distinct zone, and many microbes shared across its whole intestine are not found in the\n                      <jats:italic>G. aculeatus<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      Our data supports the notion of the stomach and its distinct microbiome being an immunological gatekeeper for the gut, but also suggests that\n                      <jats:italic>S. typhle<\/jats:italic>\n                      might benefit from the additional microbes as many indicator taxa are suspected to act as mutualistic symbionts. Stomach-loss may therefore be a trade-off between improved chemical digestion capabilities and an immunological gate-keeper vs. improved microbial digestion and increased immune stimulation.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12862-026-02546-4","type":"journal-article","created":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T19:13:54Z","timestamp":1782846834000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gastrointestinal microbiota of sympatric pipefish (Syngnathus typhle) and stickleback (Gasterosteus aculeatus) indicate trade-off associated with evolutionary stomach loss"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6015-7219","authenticated-orcid":false,"given":"Ralf F.","family":"Schneider","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jule","family":"Peter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nils","family":"Newrzella","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silke-Mareike","family":"Marten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabel","family":"Tanger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivia","family":"Roth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,30]]},"reference":[{"key":"2546_CR1","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1016\/j.fsi.2019.02.007","volume":"87","author":"S Bilal","year":"2019","unstructured":"Bilal S, Lie KK, Dalum AS, Karlsen OA, Hordvik I. 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