Ruminants such as cows, sheep goats and deer are named for the rumen, the first and largest stomach, and primary fermentation “tank” for these animals. The rumen microbiome is incredibly diverse and complex, with a high number of different microbes including protozoa, bacteria, fungi and archaea. The rumen affects namely feed conversion and emissions, and can also influence the health of the animal. Genomic techniques have been instrumental in the first steps towards unravelling the complexity of the rumen.
Ruminants on a grass-based diet are dependent on the ability of the rumen microbiome to break down the cellulose in this relatively nutrient-poor feed to short chain fatty acids, the primary source of energy for the grazer. Certain bacteria, such as some Fibrobacter and Ruminococcus species, are considered to be desirable due to higher ability to digest cellulose and increasing their activity should result in better ruminant performance. However, it has been difficult to actually improve yields by feeding microbes shown to be efficient cellulose converters. Competition with other microbes is thought to be the reason behind poor establishment of probiotics in ruminants.
On the other hand, some techniques to modify the ruminant microbiome have proven to be useful for animal health. For example, it is possible to avoid intestinal problems that arise from switching a grass-fed animal to a grain diet by inoculating with rumen fluid from a grain-fed animal. Anti-nutritive factors from some pasture animals can also be broken down by inoculating with bacterial strains that have been developed for this task, thus assisting in keeping ruminants healthy. Commensal microbes are essential in normal immune function of ruminants: they stimulate intestinal cells to maintain their barrier function and can block the attachment of pathogens to the gut. Microbiome modulation could strengthen these functions.