Rumen eukaryotes are the main phenotypic risk factors for larger methane emissions in dairy cattle.

•Methane emissions in dairy cattle are driven by eukaryote proportion in the rumen•Higher rumen eukaryote proportion boost methane`s concentration and intensity•Most eucaryote increased methane emissions while most bacteria reduced them•Some archaea increased methane emissions while some other reduced them•Genetic merit for methane emissions in dairy cattle could assist on its mitigation