Molecular approaches to the analysis of gastrointestinal microbial ecosystems

Molecular analyses of ribosomal sequence diversity in mammalian and avian gut ecosystems reveal that a high proportion of gut bacteria do not correspond to known, cultured species. Many of the dominant microbial colonizers of the large intestine and rumen, of which the majority are related to the Bacteroides or Firmicutes groups, are highly sensitive to oxygen or are fastidious in their growth requirements. A wide range of 'culture-independent' approaches is now available for tracking the microbial composition of gut samples, ranging from specific probes to profiling techniques that exploit ribosomal sequence information. It remains crucially important, however, to be able to relate particular phylogenetic groups to their roles in the gut, and to their impact upon the host. This can be achieved through the isolation of abundant, but previously little-studied, groups of gut microbes, through molecular analysis of shifts in microbial communities in vivo and in vitro and, in some cases, through the targeting of functionally significant genes. Examples of these approaches, as applied to the breakdown of dietary carbohydrates, the metabolism of short-chain fatty acids (SCFAs) and the spread of antibiotic resistance genes, will be used to illustrate their potential for advancing understanding of complex gut ecosystems.