Reducing methane emissions from livestock production is of great importance for the sustainable management of the Earth’s environment. Rumen microbiota play an important role in producing biogenic methane. However, knowledge of how host genetics influences variation in ruminal microbiota and their joint effects on methane emission is limited. We analyzed data from 750 dairy cows, using a Bayesian model to simultaneously assess the impact of host genetics and microbiota on host methane emission. We estimated that host genetics and microbiota explained 24% and 7%, respectively, of variation in host methane levels. In this Bayesian model, one bacterial genus explained up to 1.6% of the total microbiota variance. Further analysis was performed by a mixed linear model to estimate variance explained by host genomics in abundances of microbial genera and operational taxonomic units (OTU). Highest estimates were observed for a bacterial OTU with 33%, for an archaeal OTU with 26%, and for a microbial genus with 41% heritability. However, after multiple testing correction for the number of genera and OTUs modelled, none of the effects remained significant. We also used a mixed linear model to test effects of individual host genetic markers on microbial genera and OTUs. In this analysis, genetic markers inside host genes ABS4 and DNAJC10 were found associated with microbiota composition. We show that a Bayesian model can be utilized to model complex structure and relationship between microbiota simultaneously and their interaction with host genetics on methane emission. The host genome explains a significant fraction of between-individual variation in microbial abundance. Individual microbial taxonomic groups each only explain a small amount of variation in methane emissions. The identification of genes and genetic markers suggests that it is possible to design strategies for breeding cows with desired microbiota composition associated with phenotypes.

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