Fig. 2

R. gnavus transiently dominates the gut microbiome in IBD. a The maximum relative abundance of R. gnavus across samples (time courses) is shown for all subjects in the LSS (n = 266), Lewis et al. (n = 368), and HMP (n = 80) cohorts. While the abundance of most anaerobes are lower in IBD patients, the abundance of R. gnavus is significantly higher in IBD patients compared to controls. b Relative abundance of R. gnavus over time for IBD patients in the LSS cohort. The abundance of R. gnavus is not constantly high, but rather has transient increases in the IBD gut. c A principle coordinate analysis (PCoA) of the Bray-Curtis distance of species-level microbial communities of LSS IBD patient p8808 over 9 months. The dominant R. gnavus strain in months 4–10 and month 12 is R. gnavus clade 1, while in month 11 the dominant strain of R. gnavus is R. gnavus clade 2 (Fig. 3). Inset shows the Harvey-Bradshaw Index (HBI) score, a clinical indication of active disease and inflammation, for this patient over time. The dramatic, transient increased abundances of R. gnavus in month 11 corresponds to an increase in HBI values (i.e., disease activity). d Colony forming units of R. gnavus, Eubacterium elegans, and E. coli at 0, 1, and 3 h post-transfer to atmospheric oxygen conditions (see “Methods”). Error bars represent standard deviation. Dotted line signifies limit of detection. No colonies were detected for the obligate anaerobe E. elegans at the 1- and 3-h time points. As expected, E. coli showed growth during oxygen exposure, and interestingly, despite being classified as an obligate anaerobe, R. gnavus was able to tolerate atmospheric oxygen for several hours, which may partially explain its increased abundance in the increased oxidative stress of the IBD gut