Recent advance in the technologies to analyze the composition of bacterial communities, including pyrosequencing, has provided a much longer list of bacterial names related to human intestinal microbiota. Out of 30 phyla of the domain Bacteria and 5 phyla of the domain Archaea, 11 phyla of the domain Bacteria and 1 phylum of the domain Archaea are detected in the human intestinal tract. This paper describes the phylogenetic positions of species inhabiting the human digestive tract.
Lactic acid bacteria (LAB) are widely used in industry for various purposes, such as probiotics and starters for fermented food and for silage, and are intensively studied. The taxonomy of LAB has changed over the last two decades because of the contribution of phylogenetic analysis, based on 16S rRNA gene sequences, to the taxonomy. The number of species proposed as novel taxa classified in the group of LAB keeps growing, and, at present, 35 genera containing over 300 species are classified in the group. The species include species which were later reclassified into another (novel) genera based on their phylogenetic positions. This has resulted in taxonomic confusion among researchers. In this review, the present taxonomy of LAB is discussed. Since Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and Related Organisms in International Committee on Systematics of Prokaryotes has published recommended minimal standards for novel taxa in bifidobacteria and LAB, the recommendation is also introduced here.