In vitro incubation reveals the human overall gut microbiota composition is resilient to changes in methanogenesis

Hydrogen metabolism plays a central role in microbial fermentation. However, how hydrogenotrophic microbes impact microbiota composition and metabolite production in gut ecosystems remains largely unknown. Hence this study aims to investigate the impact of altering hydrogenotrophic activities, namely methanogenesis and sulphate reduction, on human gut microbiota composition and metabolite production. Faecal slurries from three methane excretors (MEs) and three non-methane excretors (NMEs) were inoculated into a basal medium with pectin or a carbohydrate mixture as substrates. Methanogenesis was inhibited by adding 2-bromoethanesulfonate to ME incubations or stimulated by adding Methanobrevibacter smithii to NME incubations. Sulphate reduction was stimulated by adding sodium sulphate to both incubations. Our observations revealed that microbial richness and composition, and propionate and methane production differed significantly between MEs and NMEs. Lower hydrogen concentrations were observed in MEs compared to NMEs in the incubations with pectin, but not with the carbohydrate mixture. Remarkably, sulphate was not consumed in either ME or NME incubations. Adding M. smithii to the NME inocula resulted in its persistence in the community and methane production during incubations. The addition of 2-bromoethanesulfonate inhibited methane production in the ME incubations, accompanied with a lower relative abundance of methanogens when pectin was used as substrate. However, altering methanogenesis did not significantly change overall microbiota composition and short-chain fat acid production in MEs and NMEs. These findings suggest that methanogens can occupy a niche in a microbiota that originally lacks methanogens, but that modulating methanogenesis has a minor effect on overall microbiota composition and activity.