Diversity, Dynamics, and Drivers of the Rumen Microbial Ecosystem

Ruminant production systems exist at the nexus of vital issues confronting society, including emerging antibiotic resistance, global warming, and feeding a growing population. The rumen is host to a complex microbial community that drives degradation and fermentation processes that yield metabolic energy for the host. The rumen microbiome is estimated to provide ~70% of a ruminant’s caloric needs. Rumen microbes are therefore vital to ruminant health and productivity, and in turn, are central to the sustainability of ruminant agriculture. However, our knowledge of the dynamics, ecological drivers, and genomic diversity of the rumen microbiome is limited. Through multiple investigations, we attempt to increase our fundamental understanding of rumen microbial ecology. As a result, we demonstrate: (a) rumen bacterial communities can be acclimated to high concentrate diets faster than traditional adaptation programs, (b) total digestible nutrients is the primary ecological driver of rumen bacterial and viral populations, (c) viral-encoded auxiliary metabolism genes modulate rumen carbon metabolism, and (d) the reconstruction of 2,150 microbial genomes improves the genomic representation for rumen microbial taxa. Further, mining recovered metagenome-assembled genomes suggests rumen microbes encode diverse biosynthetic gene clusters and are a rich source of natural products for manipulating rumen fermentation. We anticipate improved genomic characterization of rumen microbes integrated with foundational knowledge on the dynamics and drivers of the ecosystem can lead to the development of more mechanistic understandings of the rumen microbiome