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While numerous studies report sex differences in fecal microbial communities, the role of the reproductive axis in this differentiation is unclear and it is unknown how sex differentiation affects microbial diversity in specific regions of the small and large intestine.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We used a genetic hypogonadal mouse model that does not produce sex steroids or go through puberty to investigate how sex and the reproductive axis impact bacterial diversity within the intestine. Using 16S rRNA gene sequencing, we analyzed alpha and beta diversity and taxonomic composition of fecal and intestinal communities from the lumen and mucosa of the duodenum, ileum, and cecum from adult female (<jats:italic>n<\/jats:italic>\u2009=\u200920) and male (<jats:italic>n<\/jats:italic>\u2009=\u200920) wild-type mice and female (<jats:italic>n<\/jats:italic>\u2009=\u200917) and male (<jats:italic>n<\/jats:italic>\u2009=\u200920) hypogonadal mice.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Both sex and reproductive axis inactivation altered bacterial composition in an intestinal section and niche-specific manner. Hypogonadism was significantly associated with bacteria from the<jats:italic>Bacteroidaceae,<\/jats:italic><jats:italic>Eggerthellaceae,<\/jats:italic><jats:italic>Muribaculaceae<\/jats:italic>, and<jats:italic>Rikenellaceae<\/jats:italic>families<jats:italic>,<\/jats:italic>which have genes for bile acid metabolism and mucin degradation. Microbial balances between males and females and between hypogonadal and wild-type mice were also intestinal section-specific. In addition, we identified 3 bacterial genera (<jats:italic>Escherichia<\/jats:italic><jats:italic>Shigella<\/jats:italic>,<jats:italic>Lachnoclostridium<\/jats:italic>, and<jats:italic>Eggerthellaceae<\/jats:italic><jats:italic>genus<\/jats:italic>) with higher abundance in wild-type female mice throughout the intestinal tract compared to both wild-type male and hypogonadal female mice, indicating that activation of the reproductive axis leads to female-specific differentiation of the gut microbiome. Our results also implicated factors independent of the reproductive axis (i.e., sex chromosomes) in shaping sex differences in intestinal communities. Additionally, our detailed profile of intestinal communities showed that fecal samples do not reflect bacterial diversity in the small intestine.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our results indicate that sex differences in the gut microbiome are intestinal niche-specific and that sampling feces or the large intestine may miss significant sex effects in the small intestine. These results strongly support the need to consider both sex and reproductive status when studying the gut microbiome and while developing microbial-based therapies.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13293-023-00564-1","type":"journal-article","created":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T11:01:50Z","timestamp":1699268510000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities"],"prefix":"10.1186","volume":"14","author":[{"given":"Laura","family":"Sisk-Hackworth","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jada","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lillian","family":"Sau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew A.","family":"Levine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lai Ying Ivy","family":"Tam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aishwarya","family":"Ramesh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reeya S.","family":"Shah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelyn T.","family":"Kelley-Thackray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophia","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott T.","family":"Kelley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6672-6117","authenticated-orcid":false,"given":"Varykina G.","family":"Thackray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,11,6]]},"reference":[{"key":"564_CR1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.604000","author":"R Shepherd","year":"2021","unstructured":"Shepherd R, Cheung AS, Pang K, Saffery R, Novakovic B. 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