Characterisation and quantification of the microbial populations of the rumen
Already more than 3000 bacterial 16S rRNA gene sequences of rumen origin have been archived in public databases. Molecular-based approaches have been adapted more recently to protozoa and archaea, which also appear to be more diverse than once thought.
Although providing a much more comprehensive description of bacterial diversity, sequencing approaches have limitations when extended to functional diversity and ecology. Quantification of important groups or species using molecular-based procedures can help explain their role in ruminal metabolism but also to provide perspective for more qualitative approaches. Herein, we have reviewed recent microbial ecology studies, mostly those using molecular biology approaches, with an emphasis on quantitative aspects and the relationship
to ruminant nutrition. Advancing knowledge has led to more questions about how microbes interact in communities within different rumen compartments and even among animals fed similar diets. We suggest that future efforts should be directed toward the cultivation of the previously uncultured bacteria and the use of high throughput strategies to further delineate true diversity and function of rumen microbial populations under different dietary conditions. Ruminant animal production should become increasingly more efficient when rumen microbial ecology and nutrition studies are integrated, particularly if research efforts are coordinated among laboratories.