Energy generation drives gut colonization by Bilophila wadsworthia

High-fat diets alter the gut microbiota composition and stimulate proliferation of the sulfidogenic bacterium Bilophila wadsworthia (Bw). Proliferation of B. wadsworthia is linked to gut inflammation, dysfunction of the intestinal barrier and bile acid metabolism but the genetic basis for its colonization of the gut remains largely unknown. In this study, we identified genes that facilitate gut colonization by B. wadsworthia under a high-fat diet, either with or without a simplified humanized microbial consortium (SIHUMI), by using a combination of ‘omics’ approaches, including genome-wide transposon mutagenesis, metatranscriptomics and untargeted metabolomics. Comparisons between mutants present in culture and mutants in the gut revealed 32 genes essential for gut colonization. These included two gene clusters related to bacterial microcompartment (BMC) formation and function, and a NADH dehydrogenase (hdrABC-flxABCD) important for energy metabolism in anaerobes. BMCs allow B. wadsworthia to metabolise the organosulfonate compounds taurine and isethionate (abundant in the mammalian gut) releasing H2S, acetate and possibly ethanol. Although the H2S concentration and B. wadsworthia abundance were at their highest in the absence of the SIHUMI, detrimental impacts on the host were exacerbated in the presence of the SIHUMI, based on gut permeability, the abundance of pro-inflammatory cytokines (IL-1a, IFN-G) and increased infiltration of macrophages in the liver. More genes were required by B. wadsworthia for gut colonization when they were grown with the SIHUMI consortia compared with growth in monoculture; the same was true for their ability to synthesise nucleotides and histidine. This suggests that microbial community composition plays a key role in modulation of the activity of this pathobiont.