Genome sequencing and the rumen microbiome

Microbial genome sequencing has had an enormous impact on our understanding of many biological systems, including the identity, relationships and functions of the resident microbes of the rumen. The availability of genomic information has enhanced our understanding of metabolic activities these microbes possess, and fuelled the generation of hypotheses for mechanisms driving interactions both within the microbiome and the host. Since the first rumen microbial genome was sequenced in 2003, over 500 genomes from cultured isolates and over 5,000 genomes from metagenomic data studies have revealed a complex picture of how their genomic repertoire are formed by their ecological interactions during the breakdown of the plant material consumed by the host. Yet this picture remains incomplete since many organisms known to be present are missing from the genomic database, compounded by the lack of comprehensive databases to leverage this information to its full extent. A complete understanding of the rumen microbiome relies on these gaps being addressed.