In cattle a specialized organ has evolved (the rumen) housing a community of microorganisms that in concert degrade plant materials into utilizable substrates by the host animal. These organisms, beginning with fiber-degraders, convert the complex structure of fiber into increasingly simpler compounds. Ruminococcus flavefaciens is a fiber-degrading microorganism that expresses cellulosome-complexes which are enzymatic assemblages exhibiting coordinated fiber-degrading activities. Analysis of the genome sequence of one of the strains indicates that a large number of the ORFs that encode enzymes related to fiber-degradation may interact in a cellulosome-type fashion indicating its potential for degrading more resistant forms of fiber. However, optimal activity of fiber-degrading microorganisms is dependent upon the remainder of the microbial community to "pull" on this metabolism by consuming the metabolic end-products. In this manner, the process can be viewed as a simple chemostat (or digester) system. There is an influx of substrate (or feed) at a periodic rate and a concomitant efflux of converted biomass (or waste) at a constant rate. How can we improve our understanding of the function of a "simple" system that is actually a complex collection of microorganisms (numbering 10^11 cells per mL and comprised of several hundred different species) subsisting within a larger host organism? Molecular-based microbial ecology approaches have been transformed by the high-throughput application of methods including T-RFLP, clone libraries, and, more recently, pyrosequencing. These tools yield data leading to insightful models of complex systems such as the microbial populations inhabiting the gastrointestinal tract of mammals - whether they be as small as the laboratory mouse or as large as cattle. Understanding changes in the structure of microbial communities is an important and crucial step towards framing the functional data gained from metagenomic sequence surveys.