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Our study provides substantial evidence that the host genome affects the comprehensive function of the microbiome in the rumen of bovines. Of 1,107/225/1,141 rumen microbial genera/metagenome assembled uncultured genomes (RUGs)/genes identified from whole metagenomics sequencing, 194/14/337 had significant host genomic effects (heritabilities ranging from 0.13 to 0.61), revealing that substantial variation of the microbiome is under host genomic control. We found 29/22/115 microbial genera/RUGs/genes host-genomically correlated (|0.59| to |0.93|) with emissions of the potent greenhouse gas methane (CH 4 ), highlighting the strength of a common host genomic control of specific microbial processes and CH 4 . Only one of these microbial genes was directly involved in methanogenesis ( cofG ), whereas others were involved in providing substrates for archaea (e.g.  bcd  and  pccB ), important microbial interspecies communication mechanisms ( ABC.PE.P ), host-microbiome interaction ( TSTA3 ) and genetic information processes ( RP-L35 ). In our population, selection based on abundances of the 30 most informative microbial genes provided a mitigation potential of 17% of mean CH 4  emissions per generation, which is higher than for selection based on measured CH 4  using respiration chambers (13%), indicating the high potential of microbiome-driven breeding to cumulatively reduce CH 4  emissions and mitigate climate change.

Bovine host genome acts on rumen microbiome function linked to methane emissions