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The microorganisms that colonize the digestive tract, or microbiota, are of considerable importance to the host. The microbiota influences metabolism, protects against pathogens and food toxins, stimulates the immune system, promotes the development of body tissues, influences behaviour, and plays a fundamental role in nutrition.
For ruminants, the microbiota present in the rumen converts into milk and meat, foods of high nutritional value that cannot be consumed by humans or other farm animals because they are not digestible. However, the fermentation of food by rumen microorganisms is also responsible for the production of methane and nitrogen-rich waste products.

The objective of this work was to establish a catalog of prokaryotic genes (i.e., bacteria and methane-producing archaea) present in the bovine rumen. This inventory was carried out using a metagenomic approach, i.e. by simultaneous large-scale sequencing of the genes of the microbial species present.
This sequencing made it possible to identify 13,825,880 non-redundant prokaryotic genes. These data significantly increase the number of genes known as rumen microbes. Compared to catalogs of human, porcine or mouse intestinal metagenomes, the rumen metagenome is notably more diverse and richer in functions and microbial species associated with the degradation of plant cell wall material and methane production. This catalog also enriches the available data on the enzymes that degrade carbohydrates in the rumen.
By using an independent data set from a group of 77 cattle fed 4 common diets, the researchers found that less than 0.1% of the genes were shared by all animals. These results, however, show significant redundancy for other functions, with, for example, 63% of the genes common for functions listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
Diet induces differences in the relative abundance of genes rather than the presence or absence of genes, which explains the great ability of cattle to adapt quickly to changes in diet.
The resulting catalog is an important resource to improve our understanding of the biological processes involved in the degradation of cellulosic feeds. This catalog will be completed as new data become available.