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