Abstract
Instead of making classifications based on physiological and biochemical traits, comparative analysis of the 16S rRNA sequences has been used to explore the phylogenetic relationships of bacteria. The establishment of this new taxonomy has also brought new insight to the field of microbiology ecology. 16S rRNA molecules are used as the marker because: they are universally present in all organisms; they contain sufficient information for reliable phylogenetic analyses (more than 1,000 nucleotides); they are easy to handle with a high degree of precision to characterize; and the fact that the sequences of almost all species are found in public databases. To discuss the relationship between a host and its flora, it is essential to know the composition and phylogeny of the intestinal bacteria. In this review, I would like to focus on the phylogeny of predominant bacteria in human intestinal flora such as the Clostridium coccoides group, the Clostridium leptum subgroup, Bacteroides, Bifidobacterium, and the Atopobium cluster, to identify which species are assigned to these bacterial groups.
