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Background  Recent metagenomic analyses have revealed dysbiosis of the gut microbiota of ulcerative colitis (UC) patients. However, the impacts of this dysbiosis are not fully understood, particularly at the strain level.    Results  We perform whole-genome shotgun sequencing of fecal DNA extracts from 13 healthy donors and 16 UC and 8 Crohn’s disease (CD) patients. The microbiota of UC and CD patients is taxonomically and functionally divergent from that of healthy donors, with  E. faecium  being the most differentially abundant species between the two microbial communities. Transplantation of feces from UC or CD patients into  Il10  −/−  mice promotes pathological inflammation and cytokine expression in the mouse colon, although distinct cytokine expression profiles are observed between UC and CD. Unlike isolates derived from healthy donors,  E. faecium  isolates from the feces of UC patients, along with  E. faecium  strain ATCC 19434, promotes colitis and colonic cytokine expression. Inflammatory  E. faecium  strains, including ATCC 19434 and a UC-derived strain, cluster separately from commercially available probiotic strains based on whole-genome shotgun sequencing analysis. The presence of  E. faecium  in fecal samples is associated with large disease extent and the need for multiple medications in UC patients.    Conclusions   E. faecium  strains derived from UC patients display an inflammatory genotype that causes colitis.

Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host