Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning

Enteric methane emissions are energy losses from farmed ruminants and contribute to global warming. Diverting electrons and H2 flow toward beneficial fermentation products would mitigate ruminal methane emissions while improving feed efficiency. Acetogens can direct H2 and electrons to acetate production via the Wood-Ljungdahl pathway, but methanogens have more competitive H2 affinities. Thus, it is unclear how acetogenesis contributes to the rumen fermentation. An analysis of 2102 globally derived rumen metagenomes from multiple ruminant species revealed that putative acetogens were phylogenetically diverse and capable of using carbohydrates or H2 as electron donors. The metabolic versatility of these acetogens may enable them to outcompete methanogens with lower versatility. Through animal trials, in vitro experiments, and DNA stable isotope probing, we verified the presence of diverse acetogens in beef cattle rumens and revealed that their niche partitioning is driven by contrasting fiber-rich and starch-rich diets. A fiber-rich diet enriched heterotrophic acetogens, which increased acetate formation while decreasing methane production. Overall, this study highlights the overlooked heterotrophy of acetogens in the rumen and their potential for mitigating enteric methane emissions.