Bacteroidetes

Bacteroidetes
Scientific classification
Domain:	Bacteria
Phylum:	Bacteroidetes Krieg et al. 2012
Classes
Bifissio spartinae ♠ Xin & Zhou 2001 ‘Candidatus Amoebophilus’Horn et al. 2001 ‘Candidatus Cardinium’ Zchori-Fein et al. 2004 ‘Candidatus Paenicardinium’ Noel and Atibalentja 2006 Toxothrix ♪ Molisch 1925 Venteria ♠ Bae 2005 Bacteroidia Krieg 2012 Bacteroidales Krieg 2012 ‘Candidatus Armantifilum’ Desai et al. 2010 ‘Candidatus Azobacteroides’ ‘Candidatus Symbiothrix’ Hongoh et al. 2007 ‘Candidatus Vestibaculum’ Stingl et al. 2004 Sunxiuqinia Qu et al. 2011 Bacteroidaceae Pribram 1933 Marinilabiaceae Ludwig et al. 2012 Porphyromonadaceae Krieg 2012 Prevotellaceae Krieg 2012 Rikenellaceae Krieg et al. 2012 Cytophagia Nakagawa 2012 Cytophagales Leadbetter 1974 Cyclobacteriaceae Nedashkovskaya and Ludwig 2012 Cytophagaceae Stanier 1940 Flammeovirgaceae Yoon et al. 2011 Rhodothermaceae Ludwig et al. 2012 Flavobacteriia Bernardet 2012 Flavobacteriales Bernardet 2012 Blattabacteriaceae Kambhampati 2012 Cryomorphaceae Bowman et al. 2003 Flavobacteriaceae Reichenbach et al. 1992 emend. Bernardet et al. 2002 Schleiferiaceae Albuquerque et al. 2011 Sphingobacteria Kämpfer 2012 Sphingobacteriales Kämpfer 2012 Chitinophagaceae Kämpfer et al. 2011 Saprospiraceae Krieg et al. 2012 Sphingobacteriaceae Steyn et al. 1998

The phylum Bacteroidetes is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, 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.^[1]

Members of the genus Bacteroides are opportunistic pathogens. Rarely are members of the other two classes pathogenic to humans.

This phylum is sometimes grouped with Chlorobi, Fibrobacteres, Gemmatimonadates, Caldithrix, and marine group A to form the FCB group or superphylum.^[2] In the alternative classification system proposed by Cavalier-Smith, this taxon is instead a class in the Sphingobacteria phylum.

Genomics

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.^[2] Additionally, four 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 eight 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 because 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 three-amino-acid deletion in ClpB chaperone 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 three-amino-acid deletion serve as molecular markers for the Bacteroidetes.^[2]

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, three proteins have been identified which are uniquely shared by virtually all members of the Bacteroidetes and Chlorobi phyla.^[2] The sharing of these three proteins is significant because other than them, 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 phyla. The presence of these molecular signatures supports their close relationship.^[2][3] 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^[3] These phyla also branch in the same position based upon conserved signature indels in a number of important proteins.^[4] 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.^[2][3]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature^[5] and National Center for Biotechnology Information (NCBI)^[6] and the phylogeny is based on 16S rRNA-based LTP release 111 by 'The All-Species Living Tree' Project.^[7]

?Bifissio spartinae ♠ Xin & Zhou 2001 ?‘Candidatus Amoebophilus asiaticus’Horn et al. 2001 ?‘Candidatus Cardinium hertigii’ Zchori-Fein et al. 2004 ?‘Candidatus Paenicardinium endonii’ Noel and Atibalentja 2006 ?Toxothrix trichogenes ♪ (Cholodny 1924) Beger 1953 ?Venteria marina ♠ Bae 2005 Rhodothermaceae Balneola-Gracilimonas clade Cytophagales Cytophagaceae 2 Bacteroidetes Order III ''incertae sedis'' [incl. Flexibacter species group 2] Flammeovirgaceae 1 Microscilla clade [incl. Flexibacter species group 3] Flammeovirgaceae 2 [incl. Ekhidna lutea] Fulvivirga-Reichenbachiella clade Cesiribacter-Marivirga clade Cytophagaceae 1 Cytophagaceae 3 Cytophagaceae 4 Cyclobacteriaceae [incl. Litoribacter ruber & Rhodonellum psychrophilum] Sphingobacteriaceae [incl. Flavobacterium mizutaii] Saprospiraceae Chitinophagaceae Cryomorphaceae 1 [incl. Schleiferia thermophila] Flavobacteriales ?'Candidatus Sulcia muelleri' Moran et al. 2005 ?'Candidatus Uzinura diaspidicola' Gruwell et al. 2007 ?Phaeocystidibacter luteus ?Salinirepens amamiensis ?Blattabacteriaceae Cryomorphaceae 2 Flavobacteriaceae Bacteroidales ?‘Candidatus Armantifilum devescovinae’ Desai et al. 2010 ?‘Candidatus Azobacteroides pseudotrichonymphae’ ?‘Candidatus Symbiothrix dinenymphae’ Hongoh et al. 2007 ?‘Candidatus Vestibaculum illigatum’ Stingl et al. 2004 ?Alkalitalea saponilacus ♣ ?Thermophagus xiamenensis ♣ Rikenellaceae Cytophaga fermentans Bachmann 1955 Marinifilum fragile Na et al. 2009 Sunxiuqinia elliptica Qu et al. 2011 Meniscus glaucopis Irgens 1977 Prolixibacter bellariavorans Holmes et al. 2007 Alkaliflexus imshenetskii Zhilina et al. 2005 Marinilabiliaceae 1 Marinilabiliaceae 2 [incl. Cytophaga xylanolytica] Porphyromonadaceae 2 Porphyromonadaceae 1 Bacteroidaceae [incl. Prevotellaceae]

Notes
♠ Strains found at the National Center for Biotechnology Information, 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

References

1. Krieg, N.R.; Ludwig, W.; Whitman, W.B.; Hedlund, B.P.; Paster, B.J.; Staley, J.T.; Ward, N.; Brown, D.; Parte, A. (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.
2. Gupta, R. S.; 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.
3. 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. PMID 15239383.
4. 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". Microbiology 147: 2611–22. doi:10.1099/00221287-147-9-2611.
5. J.P. Euzéby. "Bacteroidetes". List of Prokaryotic names with Standing in Nomenclature. Retrieved 2013-03-20.
6. Sayers; et al. "Bacteroidetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2013-03-20.
7. 'The All-Species Living Tree' Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.

External links

• Phylogenomics and Evolutionary Studies on Bacteriodetes, Chlorobi and Fibrobacteres Species Bacterial (Prokaryotic) Phylogeny Webpage