The phylum Bacteroidetes is composed of three large classes of Gram-negative, nonsporeforming, anaerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments and sea water as well as in the guts and on the skin of animals.
By far, the ones in the Bacteroidia class are the most well-studied, including the genus Bacteroides (an abundant organism in the feces of warm-blooded animals including humans), and Porphyromonas, a group of organisms inhabiting the human oral cavity. The class Bacteroidia was formerly called Bacteroidetes; as it was until recently the only class in the phylum, the name was changed in the fourth volume of Bergey's Manual of Systematic Bacteriology.
This phylum is sometimes grouped with Chlorobi, Fibrobacteres, Gemmatimonadates, Caldithrix and Marine group A to form the FCB group or superphylum. In the alternative classification system proposed by Cavalier-Smith, this taxon is instead a class in the Sphingobacteria phylum.
Comparative genomic analysis has led to the identification of 27 proteins which are present in most species of the phylum Bacteroidetes. Of these, one protein is found in all sequenced Bacteroidetes species, while two other proteins are found in all sequenced species with the exception of those from the genus Bacteroides. The absence of these two proteins in this genus is likely due to selective gene loss. Additionally, 4 proteins have been identified which are present in all Bacteroidetes species except Cytophaga hutchinsonii; this is again likely due to selective gene loss. A further 8 proteins have been identified which are present in all sequenced Bacteroidetes genomes except Salinibacter ruber. The absence of these proteins may be due to selective gene loss, or, due to the fact that S. ruber branches very deeply, the genes for these proteins may have evolved after the divergence of S. ruber. A conserved signature indel has also been identified; this 3 amino acid deletion in ClpB protease is present in all species of the Bacteroidetes phylum except S. ruber. This deletion is also found in one Chlorobi species and one Archaeum species, which is likely due to horizontal gene transfer. These 27 proteins and the 3 amino acid deletion serve as molecular markers for the phylum Bacteroidetes.
Relatedness of Bacteroidetes, Chlorobi and Fibrobacteres Phyla
Species from the Bacteroidetes and Chlorobi phyla branch very closely together in phylogenetic trees, indicating a close relationship. Through the use of comparative genomic analysis, 3 proteins have been identified which are uniquely shared by virtually all members of the Bacteroidetes and Chlorobi phyla. The sharing of these 3 proteins is significant because other than these 3 proteins, no proteins from either the Bacteroidetes or Chlorobi phyla are shared by any other groups of bacteria. Several conserved signature indels have also been identified which are uniquely shared by members of the Bacteroidetes and Chlorobi phyla. The presence of these molecular signatures supports the close relationship of the Bacteroidetes and Chlorobi phyla. Additionally, the phylum Fibrobacteres is indicated to be specifically related to these two phyla. A clade consisting of these three phyla is strongly supported by phylogenetic analyses based upon a number of different proteins These phyla also branch in the same position based upon conserved signature indels in a number of important proteins. Lastly and most importantly, two conserved signature indels (in the RpoC protein and in serine hydroxymethyltransferase) and one signature protein PG00081 have been identified that are uniquely shared by all of the species from these three phyla. All of these results provide compelling evidence that the species from these three phyla shared a common ancestor exclusive of all other bacteria, and it has been proposed that they should all recognized as part of a single “FCB” superphylum.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)  and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 111 by 'The All-Species Living Tree' Project 
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the LPSN
♪ Prokaryotes where no pure (axenic) cultures are isolated or available; i.e., not cultivated or cannot be sustained in culture for more than a few serial passages
- Krieg, N.R.; Ludwig, W.; Whitman, W.B.; Hedlund, B.P.; Paster, B.J.; Staley, J.T.; Ward, N.; Brown, D. et al. (November 24, 2010) [1984(Williams & Wilkins)]. George M. Garrity, ed. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Bergey's Manual of Systematic Bacteriology 4 (2nd ed.). New York: Springer. p. 908. ISBN 978-0-387-95042-6. British Library no. GBA561951.
- Gupta, R. S. and Lorenzini, E. (2007). Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species" BMC Evolutionary Biology 7:71. doi:10.1186/1471-2148-7-71
- Gupta, R. S. (2004). The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes. Critical Reviews in Microbiology. 30:123-140. doi:10.1080/10408410490435133
- Griffiths E, Gupta RS. (2001) The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga- Flavobacterium-Bacteroides division" Microbiology147:2611-22.
- J.P. Euzéby. "Bacteroidetes". List of Prokaryotic names with Standing in Nomenclature (LPSN) . Retrieved 2013-03-20.
- Sayers et al. "Bacteroidetes". National Center for Biotechnology Information (NCBI) taxonomy database . Retrieved 2013-03-20.
- 'The All-Species Living Tree' Project."16S rRNA-based LTP release 111 (full tree)". Silva Comprehensive Ribosomal RNA Database . Retrieved 2013-03-20.
- Phylogenomics and Evolutionary Studies on Bacteriodetes, Chlorobi and Fibrobacteres Species Bacterial (Prokaryotic) Phylogeny Webpage