Protozoal populations drive system-wide variation in the rumen microbiome

While rapid progress has been made to characterize the bacterial and archaeal populations of the rumen microbiome, insight into how they interact with keystone protozoal species remains elusive. Here, we reveal two distinct rumen community types (RCT-A and RCT-B) that are not strongly associated with host phenotype nor genotype but instead linked to protozoal community patterns. We leveraged a series of multi-omic datasets to show that the dominantEpidiniumspp. in animals with RCT-B employ a plethora of fiber-degrading enzymes that present enrichedPrevotellaspp. a favorable carbon landscape to forage upon. Conversely, animals with RCT-A, dominated by generaIsotrichaandEntodinium, harbor a more even distribution of fiber, protein, and amino acid metabolizers, reflected by higher detection of metabolites from both protozoal and bacterial activity. We reveal that microbiome variation transcends key protozoal and bacterial populations, which should act as an important consideration for future development of microbiome-based technologies.