Molecular techniques for monitoring bacterial and bacteriophage populations in the rumen

ABSTRACT Molecular techniques are increasingly being used in microbial ecology to identify microorganisms, infer phylogenetic relationships, and describe community structure. We have used rRNA sequence information to develop a competitive PCR technique which enumerates proteolytic bacterial populations from the forestomach of pasture-grazed ruminants. PCR primer pairs, which circumscribe several proteolytic rumen bacterial populations, were used in co-amplifications of target and internal control DNAs, to quantify individual microbial populations. The results from enumerations in pasture-fed animals will be discussed in relation to the sensitivity, specificity and quantitative aspects of the technique. Rumen bacteriophage also impact significantly on rumen metabolism and are being quantified by DNA-based techniques. Studies using pulsed-field gel electrophoresis and laser densitometry of purified phage DNA have shown large variations in ruminal bacteriophage numbers and bacteriophage types. These molecular techniques provide better descriptions of individual ruminal populations and eventually will allow for a complete description of the rumen ecosystem