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To understand the role of the microbiome in GI diseases, we characterized the gut microbiome of 91 healthy marmosets (303 samples) and 59 marmosets diagnosed with inflammatory bowel disease (IBD) (200 samples). Healthy marmosets exhibited \u201chumanized,\u201d<jats:italic>Bacteroidetes<\/jats:italic>-dominant microbiomes. After up to 2 years of standardized diet, housing and husbandry, marmoset microbiomes could be classified into four distinct marmoset sources based on<jats:italic>Prevotella<\/jats:italic>and<jats:italic>Bacteroides<\/jats:italic>levels. Using a random forest (RF) model, marmosets were classified by source with an accuracy of 93% with 100% sensitivity and 95% specificity using abundance data from 4<jats:italic>Prevotellaceae<\/jats:italic>amplicon sequence variants (ASVs), as well as single ASVs from<jats:italic>Coprobacter, Parabacteroides, Paraprevotella, Phascolarctobacterium, Oribacterium<\/jats:italic>and<jats:italic>Fusobacterium.<\/jats:italic>A single dysbiotic IBD state was not found across all marmoset sources, but IBD was associated with lower alpha diversity and a lower<jats:italic>Bacteroides<\/jats:italic>:<jats:italic>Prevotella copri<\/jats:italic>ratio within each source. IBD was highest in a<jats:italic>Prevotella<\/jats:italic>-dominant cohort, and consistent with<jats:italic>Prevotella<\/jats:italic>-linked diseases, pro-inflammatory genes in the jejunum were upregulated. RF analysis of serum biomarkers identified serum calcium, hemoglobin and red blood cell (RBC) counts as potential biomarkers for marmoset IBD. This study characterizes the microbiome of healthy captive common marmosets and demonstrates that source-specific microbiomes can be retained despite standardized diets and husbandry practices. Marmosets with IBD had decreased alpha diversity and a shift in the ratio of<jats:italic>Bacteroides:Prevotella copri<\/jats:italic>compared to healthy marmosets<jats:italic>.<\/jats:italic><\/jats:p>","DOI":"10.1038\/s41598-022-08255-4","type":"journal-article","created":{"date-parts":[[2022,3,15]],"date-time":"2022-03-15T12:04:42Z","timestamp":1647345882000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Analysis of gut microbiome profiles in common marmosets (Callithrix jacchus) in health and intestinal disease"],"prefix":"10.1038","volume":"12","author":[{"given":"Alexander","family":"Sheh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen C.","family":"Artim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monika A.","family":"Burns","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Arturo","family":"Molina-Mora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary Anne","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"JoAnn","family":"Dzink-Fox","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sureshkumar","family":"Muthupalani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James G.","family":"Fox","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,3,15]]},"reference":[{"key":"8255_CR1","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/567143","author":"CN Ross","year":"2012","unstructured":"Ross, C. 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