Common Marmoset Gut Microbiome Profiles in Health and Intestinal Disease

Chronic gastrointestinal (GI) diseases are the most common diseases in captive marmosets. The gut microbiome of healthy (n=91), inflammatory bowel disease (IBD) (n=59), and duodenal ulcer/stricture (n=23) captive marmosets was characterized. Healthy marmosets exhibited a "humanized," Bacteroidetes-dominant microbiome. Despite standardized conditions, cohorts subdivided into Prevotella- and Bacteroides-dominant groups based on marmoset source. IBD was highest in a Prevotella-dominant cohort while strictures were highest in a Bacteroides-dominant cohort. Stricture-associated dysbiosis was characterized by Anaerobiospirillum loss and Clostridium perfringens increases. Stricture tissue presented upregulation of lipid metabolism genes and increased abundance of C. perfringens, a causative agent of GI diseases and intestinal strictures in humans. IBD was associated with a lower Bacteroides:P. copri ratio within each source. Consistent with Prevotella-linked diseases, pro-inflammatory genes were upregulated. This report highlights the humanization of the captive marmoset microbiome and its potential as a "humanized" animal model of C. perfringens-induced enteritis/strictures and P. copri-associated IBD.