A MECHANISTIC VIEW OF METHANOGENIC MODULATION IN THE RUMEN

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 ingested plant material. We used extensive metabolomic analysis together with in vitro microbiology approaches and whole-genome sequencing of a methanogen from the order Methanomicrobiales that was greatly affected by dietary change in our experiments. We demonstrate that redox potential changes are induced by dietary shift and that this methanogen is directly affected by them. Furthermore, its genetic and metabolic architecture revealed unique genomic signatures encoding antioxidative proteins, explaining its redox dependent behavior. Metabolic modeling of another 415 microbial genomes from various phylogenetic groups that also change with diet, revealed that these signatures are apparent in these organisms and could cluster them according to their diet response. Based on our overall findings we propose redox to be affected by dietary change and to have a vast effect on the rumen microbial community, selecting for microbial taxa with specific genomic signatures. Our study, which encompasses multiple experimental approaches, highlights redox potential as a pivotal factor that could serve as a sculpturing force of community assembly within anaerobic gut microbial communities. Therefore, the current results may provide a stepping stone for future manipulations as well as cultivability of microbial communities not only in the rumen environment, but also in other gut environments.