| Bacteroidetes |
| Scientific classification |
| Domain: |
Bacteria |
| Phylum: |
Bacteroidetes
Krieg et al. 2012 |
| Classes |
- Rhodothermia
- Balneolia
- Cytophagia
- Sphingobacteria
- "Chitinophagia"
- Bacteroidia
- Flavobacteriia
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| Synonyms |
- Bacteroidaeota Oren et al. 2015
- Rhodothermaeota Munoz, Rossello-Mora & Amann 2016
- Saprospirae
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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. Bacteroidetes spp. are part of normal, healthy placental microbiome.[1][2]
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.[3]
Some members of the genus Bacteroides are opportunistic pathogens. Rarely are members of the other two classes pathogenic to humans.[which?]
This phylum is sometimes grouped with Chlorobi, Fibrobacteres, Gemmatimonadates, Caldithrix, and marine group A to form the FCB group or superphylum.[4] In the alternative classification system proposed by Cavalier-Smith, this taxon is instead a class in the Sphingobacteria phylum.
Contents
- 1 Genomics
- 1.1 Relatedness of Bacteroidetes, Chlorobi and Fibrobacteres phyla
- 2 Phylogeny
- 3 Taxonomy
- 4 References
- 5 External links
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.[4] 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.[4]
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.[4] 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.[4][5] 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[5] These phyla also branch in the same position based upon conserved signature indels in a number of important proteins.[6] 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.[4][5]
Phylogeny
The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project.[7]
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| Rhodothermaeota |
Rhodothermaceae
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| Bacteroidaeota |
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Balneolaceae
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| Cytophagales |
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"Hymenobacteraceae"
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"Thermonemataceae"
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"Persicobacteraceae"
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Flammeovirgaceae 1
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Cytophagaceae 2 [incl. Flexibacter species group 3]
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Flammeovirgaceae 2 [incl. Ekhidna lutea]
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Flammeovirgaceae 3
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Flammeovirgaceae 4 [Catalimonadaceae; Mooreiaceae]
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Cytophagaceae 1
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Cytophagaceae 3
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Cytophagaceae 4
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Cyclobacteriaceae
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| Sphingobacteriales |
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Filobacteriaceae
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Sphingobacteriaceae
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| "Chitinophagales" |
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Saprospiraceae
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Chitinophagaceae
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Cryomorphaceae
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| Flavobacteriales |
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"Crocinitomicaceae"
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Flavobacteriaceae
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| Bacteroidales |
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Rikenellaceae
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Marinifilaceae
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Marinilabiliaceae 2
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Prolixibacteraceae
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Alkaliflexus imshenetskii
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Marinilabiliaceae 1
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Marinilabiliaceae 3 [incl. Cytophaga xylanolytica]
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Odoribacteraceae
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Porphyromonadaceae
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Bacteroidaceae
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Taxonomy
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[8] and National Center for Biotechnology Information (NCBI).[9]
- Genus ?"Bifissio" ♠ Xin & Zhou 2001
- Species "Bifissio spartinae" ♠ Xin & Zhou 2001
- Genus ?"Candidatus Cardinium" Zchori-Fein et al. 2004
- Species "Candidatus Cardinium hertigii" Zchori-Fein et al. 2004
- Genus ?"Candidatus Paenicardinium" Noel and Atibalentja 2006
- Species "Candidatus Paenicardinium endonii" Noel and Atibalentja 2006
- Genus ?Toxothrix ♪ Molisch 1925
- Species Toxothrix trichogenes ♪ (Cholodny 1924) Beger 1953
- Genus ?"Venteria" ♠ Bae 2005
- Species "Venteria marina" ♠ Bae 2005
- Class Rhodothermia Munoz, Rossello-Mora & Amann 2016
- Order Rhodothermales Munoz, Rossello-Mora & Amann 2016 [Bacteroidetes Order II. Incertae sedis]
- Family Rhodothermaceae Ludwig et al. 2012
- Class Balneolia Munoz, Rossello-Mora & Amann 2016
- Order Balneolales Munoz, Rossello-Mora & Amann 2016
- Family Balneolaceae Xia et al. 2016 [Balneola group]
- Class Cytophagia Nakagawa 2012
- Order Cytophagales Leadbetter 1974
- Family ?"Candidatus Amoebophilaceae" Santos-Garcia et al. 2014
- Family "Hymenobacteraceae" Munoz, Rossello-Mora & Amann 2016
- Family Cyclobacteriaceae Nedashkovskaya and Ludwig 2012 [incl. Litoribacter ruber & Rhodonellum psychrophilum]
- Family Cytophagaceae Stanier 1940
- Family Flammeovirgaceae Yoon et al. 2011 [Catalimonadaceae Choi et al. 2013; Mooreiaceae Choi et al. 2013]
- Family "Persicobacteraceae" Munoz, Rossello-Mora & Amann 2016
- Family "Thermonemataceae" Munoz, Rossello-Mora & Amann 2016 [Thermonema group; Bacteroidetes Order III. Incertae sedis; incl. Flexibacter species group 2]
- Class Sphingobacteria Kämpfer 2012
- Order Sphingobacteriales Kämpfer 2012
- Family Filobacteriaceae Ike et al. 2016
- Family Sphingobacteriaceae Steyn et al. 1998 [incl. Flavobacterium mizutaii]
- Class "Chitinophagia" Munoz, Rossello-Mora & Amann 2016
- Order "Chitinophagales" Munoz, Rossello-Mora & Amann 2016
- Family Chitinophagaceae Kämpfer et al. 2011
- Family Saprospiraceae Krieg et al. 2012
- Class Flavobacteriia Bernardet 2012
- Order Flavobacteriales Bernardet 2012
- Genus ?"Candidatus Sulcia muelleri" Moran et al. 2005
- Genus ?"Candidatus Uzinura diaspidicola" Gruwell et al. 2007
- Family ?Blattabacteriaceae Kambhampati 2012
- Family ?Ichthyobacteriaceae Takano et al. 2015
- Family "Crocinitomicaceae" Munoz, Rossello-Mora & Amann 2016
- Family Cryomorphaceae Bowman et al. 2003 [Schleiferiaceae Albuquerque et al. 2011]
- Family Flavobacteriaceae Reichenbach et al. 1992 emend. Bernardet et al. 2002
- Class Bacteroidia Krieg 2012
- Order Bacteroidales Krieg 2012
- Genus ?"Candidatus Armantifilum" Desai et al. 2010
- Genus ?"Candidatus Azobacteroides" Hongoh et al. 2008
- Genus ?"Candidatus Symbiothrix" Hongoh et al. 2007
- Genus ?Alkaliflexus imshenetskii Zhilina et al. 2005
- Family ?Balneicellaceae Fadhlaoui et al. 2016
- Family ?Lentimicrobiaceae Sun et al. 2016
- Family Bacteroidaceae Pribram 1933 [incl. Prevotellaceae Krieg 2012]
- Family Marinifilaceae Iino et al. 2014
- Family Marinilabiaceae Ludwig et al. 2012
- Family Odoribacteraceae Munoz, Rossello-Mora & Amann 2016
- Family Porphyromonadaceae Krieg 2012 [incl. Acetobacteroides hydrogenigenes]
- Family Prolixibacteraceae Huang et al. 2014 [Draconibacteriaceae Du et al. 2014; incl. Meniscus glaucopis]
- Family Rikenellaceae Krieg et al. 2012
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
- ^ Mor, Gil; Kwon, Ja-Young (2015). "Trophoblast-microbiome interaction: a new paradigm on immune regulation". American Journal of Obstetrics and Gynecology. 213 (4): S131–S137. ISSN 0002-9378. PMID 26428492. doi:10.1016/j.ajog.2015.06.039.
- ^ Todar, K. "Pathogenic E. coli". Online Textbook of Bacteriology. University of Wisconsin–Madison Department of Bacteriology. Retrieved 2007-11-30.
- ^ 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.
- ^ a b c d e f 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. PMC 1887533 . PMID 17488508. doi:10.1186/1471-2148-7-71.
- ^ a b c Gupta, R. S. (2004). "The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes". Critical Reviews in Microbiology. 30: 123–140. PMID 15239383. 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". Microbiology. 147: 2611–22. PMID 11535801. doi:10.1099/00221287-147-9-2611.
- ^ 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.
- ^ J.P. Euzéby. "Bacteroidetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
- ^ Sayers; et al. "Bacteroidetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
External links
- Phylogenomics and Evolutionary Studies on Bacteriodetes, Chlorobi and Fibrobacteres Species Bacterial (Prokaryotic) Phylogeny Webpage
- Infectious diseases
- Bacterial diseases: BV4 non-proteobacterial G- (primarily A00–A79, 001–041, 080–109)
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| Spirochaete |
| Spirochaetaceae |
| Treponema |
- Treponema pallidum
- Treponema carateum (Pinta)
- Treponema denticola
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| Borrelia |
- Borrelia burgdorferi/Borrelia afzelii
- Lyme disease
- Erythema chronicum migrans
- Neuroborreliosis
- Borrelia recurrentis (Louse borne relapsing fever)
- Borrelia hermsii/Borrelia duttoni/Borrelia parkeri (Tick borne relapsing fever)
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| Leptospiraceae |
| Leptospira |
- Leptospira interrogans (Leptospirosis)
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| Chlamydiaceae |
| Chlamydophila |
- Chlamydophila psittaci (Psittacosis)
- Chlamydophila pneumoniae
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| Chlamydia |
- Chlamydia trachomatis
- Chlamydia
- Lymphogranuloma venereum
- Trachoma
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| Bacteroidetes |
- Bacteroides fragilis
- Tannerella forsythia
- Capnocytophaga canimorsus
- Porphyromonas gingivalis
- Prevotella intermedia
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| Fusobacteria |
- Fusobacterium necrophorum (Lemierre's syndrome)
- Fusobacterium nucleatum
- Fusobacterium polymorphum
- Streptobacillus moniliformis (Rat-bite fever/Haverhill fever)
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