Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community

Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here, we addressed these questions in the rumen microbiome ecosystem – a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the degradation of the ingested plant material. Our dietary intervention experiments revealed that diet affects the most abundant taxa within the microbiome and that a specific group of methanogenic archaea of the order Methanomicrobiales is highly sensitive to its changes. Using metabolomic analyses together with in vitro microbiology approaches and whole-genome sequencing of Methanomicrobium mobile, a key species within this group, we identified that redox potential changes with diet and is the main factor that causes these dietary induced alternations in this taxa's abundance. Our genomic analysis suggests that the redox potential effect stems from a reduced number of anti-reactive oxygen species proteins coded in this taxon's genome. Our study highlights redox potential as a pivotal factor that could serve as a sculpturing force of community assembly within anaerobic gut microbial communities.