Cattle that eat the same feed and come from the same environment can emit methane (CH4), a potent greenhouse gas, at vastly different levels. An estimated 32% of anthropogenic CH4 can be traced to ‘enteric fermentation’ in livestock production. During enteric fermentation, specialized microorganisms will digest complex plant fiber to create compounds like acetate and hydrogen (H2). Some of these organisms, called methanogens, will consume and use these products to produce CH4. Emerging data suggests natural inter-animal variation in CH4 emissions could derive from host genetics or differences in rumen microbial digestion. Here, we analyze 16S rRNA gene amplicon sequencing from the rumen of twenty beef cattle of varying CH4 emission levels to look for differences in the structure and composition of their microbial communities. There was no significant difference in microbial community diversity by host CH4 emission level. Association tests at the genus and ASV levels revealed relationships between low residual CH4 emissions and the genera Megasphaera, Prevotellaceae, Ruminococcus, and Gastranaerophilales. Network analysis of the high and low CH4 communities revealed disrupted relationships between methanogens and other members of the community. The methanogens Methanobrevibacter and Candidatus Methanomethylophilus were significantly associated with Gastranaerophilales and Prevotellaceae, respectively in the low CH4 network. These interactions were absent in the high CH4 network. This suggests that the interactions of the low CH4-associated microbiome members and methanogens contributes to the reduced CH4 emissions. The findings of our work begin to explain why some cattle emit higher methane levels compared to others, and may aid in finding solutions to reduce methane emissions in cattle while keeping their feeding efficiency and meat production high.
