BackgroundHydrogen gas (H2) is a common product of carbohydrate fermentation in the human gut microbiome and its accumulation can modulate fermentation. Concentrations of colonic H2vary between individuals, raising the possibility that H2concentration 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 H2in 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 H2would 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.ResultsFor butyrogens that contained a hydrogenase, growth under a high H2atmosphere 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 ofFaecalibacterium prausnitziistrain A2-165, which does not contain a hydrogenase, was unaffected by H2or CO. In a synthetic gut microbial community, addition of the H2-consuming human gut methanogenMethanobrevibacter smithiidecreased butyrate production alongside H2concentration. Consistent with this observation,M. smithiimetabolic 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 H2production in the gut is especially high. Addition ofM. smithiito the synthetic communities also facilitated the growth ofE. rectale, resulting in decreased relative competitive fitness ofF. prausnitzii.ConclusionsH2is a regulator of fermentation in the human gut microbiome. In particular, high H2concentration 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.Video AbstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s40168-023-01565-3.