Rumen microbial genomics: from cells to genes (and back to cells)

Abstract The rumen harbours countless bacteria, archaea, ciliated protozoa, fungi and viruses: various microorganisms that have established multiplicity of relationships to efficiently digest complex plant fibres polysaccharides produce volatile fatty acids (VFAs), microbial proteins vitamins, essentials for the host’s health, growth performances. Recent studies using omics-based techniques revealed changes in microbiota are associated with ruminants’ production health parameters such as feed efficiency, methane yield, milk composition ruminal acidity. However, traditionally, microbes were unveiled anaerobic culture-based techniques, which at origin most basic concepts understanding functioning. Isolating culturing is frequently more difficult time-consuming requires training than molecular explains why culture seems be abandoned favour sequencing. Microbial cultures enable study substrate preferences product output, essential requirements, biocide susceptibilities; obtaining a pure also enables genome sequencing these strains. We propose here, after brief report published isolates, comprehensive review current advances methods identify novel discuss how mathematics could enhance our microbiology.