Abstract Background Hydrogen gas (H₂) is a common product of carbohydrate fermentation in the human gut microbiome and its accumulation can modulate fermentation. Concentrations of colonic H₂ vary between individuals, raising the possibility that H₂ concentration may be an important factor differentiating individual microbiomes and their metabolites. Butyrate-producing bacteria (butyrogens) in the human gut usually produce some combination of butyrate, lactate, formate, acetate, and H₂ in branched fermentation pathways to manage reducing power generated during the oxidation of glucose to acetate and carbon dioxide. We predicted that a high concentration of intestinal H₂ would favor the production of butyrate, lactate, and formate by the butyrogens at the expense of acetate, H₂, and CO₂. Regulation of butyrate production in the human gut is of particular interest due to its role as a mediator of colonic health through anti-inflammatory and anti-carcinogenic properties. Results For butyrogens that contained a hydrogenase, growth under a high H₂ atmosphere or in the presence of the hydrogenase inhibitor CO stimulated production of organic fermentation products that accommodate reducing power generated during glycolysis, specifically butyrate, lactate, and formate. Also as expected, production of fermentation products in cultures of Faecalibacterium prausnitzii strain A2-165, which does not contain a hydrogenase, was unaffected by H₂ or CO. In a synthetic gut microbial community, addition of the H₂-consuming human gut methanogen Methanobrevibacter smithii decreased butyrate production alongside H₂ concentration. Consistent with this observation, M. smithii metabolic activity in a large human cohort was associated with decreased fecal butyrate, but only during consumption of a resistant starch dietary supplement, suggesting the effect may be most prominent when H₂ production in the gut is especially high. Addition of M. smithii to the synthetic communities also facilitated the growth of E. rectale, resulting in decreased relative competitive fitness of F. prausnitzii. Conclusions H₂ is a regulator of fermentation in the human gut microbiome. In particular, high H₂ concentration stimulates production of the anti-inflammatory metabolite butyrate. By consuming H₂, gut methanogenesis can decrease butyrate production. These shifts in butyrate production may also impact the competitive fitness of butyrate producers in the gut microbiome.