Abstract
Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.
Highlights
Until recently, knowledge of rumen microbiology was primarily obtained using classical culture-based techniques, such as isolation, enumeration and nutritional characterization, which probably only account for 10 to 20% of the rumen microbial population
Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this paper
This paper will focus on DNA based molecular methods which have recently been developed for studying major functional groups of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective
Summary
Knowledge of rumen microbiology was primarily obtained using classical culture-based techniques, such as isolation, enumeration and nutritional characterization, which probably only account for 10 to 20% of the rumen microbial population. These traditional methods are time consuming and cumbersome, but have identified more than 200 species of bacteria and at least 100 species of protozoa and fungi inhabiting the rumen (Orpin and Joblin 1997; Stewart et al, 1998; Williams and Coleman 1998; White et al, 1999). This paper will focus on DNA based molecular methods which have recently been developed for studying major functional groups of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective
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