Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome

In our previous studies on the intestinal microbiota in irritable bowel syndrome (IBS), we identified a bacterial phylotype with higher abundance in patients suffering from diarrhea than in healthy controls. In the present work, we have isolated in pure culture strain RT94, belonging to this phylotype, determined its whole genome sequence and performed an extensive genomic analysis and phenotypical testing. This revealed strain RT94 to be a strict anaerobe apparently belonging to a novel species with only 94% similarity in the 16S rRNA gene sequence to the closest relatives Ruminococcus torques and Ruminococcus lactaris. The G + C content of strain RT94 is 45.2 mol% and the major long-chain cellular fatty acids are C16:0, C18:0 and C14:0. The isolate is metabolically versatile but not a mucus or cellulose utilizer. It produces acetate, ethanol, succinate, lactate and formate, but very little butyrate, as end products of glucose metabolism. The mechanisms underlying the association of strain RT94 with diarrhea-type IBS are discussed. •Some intestinal bacteria are associated with irritable bowel syndrome (IBS).•We have earlier identified a bacterial phylotype more prevalent in diarrhea-type IBS.•In this work, we have isolated, characterized and genome-sequenced this phylotype.•This novel anaerobic isolate, RT94, is metabolically versatile and well gut-adapted.•RT94 is closely related to Ruminococcus but should be classified in a novel genus.