Molecular Analysis of Archaea, Bacteria and Eucarya Communities in the Rumen

B. A. White, I. K.O. Cann, S. A. Kocherginskaya, R. I. Aminov, L. A. Thill, R. I. Mackie, R. Onodera

Research output: Contribution to journalReview articlepeer-review


If rumen bacteria can be manipulated to utilize nutrients (i.e., ammonia and plant cell wall carbohydrates) more completely and efficiently, the need for protein supplementation can be reduced or eliminated and the digestion of fiber in forage or agricultural residue-based diets could be enhanced. However, these approaches require a complete and accurate description of the rumen community, as well as methods for the rapid and accurate detection of microbial density, diversity, phylogeny, and gene expression. Molecular ecology techniques based on small subunit (SSU) rRNA sequences, nucleic acid probes and the polymerase chain reaction (PCR) can potentially provide a complete description of the microbial ecology of the rumen of ruminant animals. The development of these molecular tools will result in greater insights into community structure and activity of gut microbial ecosystems in relation to functional interactions between different bacteria, spatial and temporal relationships between different microorganisms and between microorganisms and feed particles. Molecular approaches based on SSU rRNA serve to evaluate the presence of specific sequences in the community and provide a link between knowledge obtained from pure cultures and the microbial populations they represent in the rumen. The successful development and application of these methods promises to provide opportunities to link distribution and identity of gastrointestinal microbes in their natural environment with their genetic potential and in situ activities. The use of approaches for assessing population dynamics as well as for assessing community functionality will result in an increased understanding and a complete description of the gastrointestinal communities of production animals fed under different dietary regimes, and lead to new strategies for improving animal growth.

Original languageEnglish (US)
Pages (from-to)129-138
Number of pages10
JournalAsian-Australasian Journal of Animal Sciences
Issue number1
StatePublished - Feb 1999


  • DGGE
  • DNA
  • Ecology
  • Molecular Analysis
  • RNA
  • Review
  • Rumen Microbes

ASJC Scopus subject areas

  • Food Science
  • Animal Science and Zoology


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