HOME
The Info List - Bacteroidetes


--- Advertisement ---



The phylum Bacteroidetes
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
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
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
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
Sphingobacteria
phylum.

Contents

1 Genomics

1.1 Relatedness of Bacteroidetes, Chlorobi
Chlorobi
and Fibrobacteres
Fibrobacteres
phyla

2 Phylogeny 3 Taxonomy 4 References 5 External links

Genomics[edit] 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
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
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
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
Bacteroidetes
phylum except S. ruber. This deletion is also found in one Chlorobi
Chlorobi
species and one Archaeum
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
Chlorobi
and Fibrobacteres
Fibrobacteres
phyla[edit] Species from the Bacteroidetes
Bacteroidetes
and Chlorobi
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
Bacteroidetes
and Chlorobi
Chlorobi
phyla.[4] The sharing of these three proteins is significant because other than them, no proteins from either the Bacteroidetes
Bacteroidetes
or Chlorobi
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
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[edit] The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project.[7]

Rhodothermaeota

Rhodothermaceae

Bacteroidaeota

Balneolaceae

Cytophagales

"Hymenobacteraceae"

"Thermonemataceae"

"Persicobacteraceae"

Flammeovirgaceae 1

Cytophagaceae 2 [incl. Flexibacter species group 3]

Flammeovirgaceae 2 [incl. Ekhidna lutea]

Flammeovirgaceae 3

Flammeovirgaceae 4 [Catalimonadaceae; Mooreiaceae]

Cytophagaceae 1

Cytophagaceae 3

Cytophagaceae 4

Cyclobacteriaceae

Sphingobacteriales

Filobacteriaceae

Sphingobacteriaceae

"Chitinophagales"

Saprospiraceae

Chitinophagaceae

Cryomorphaceae

Flavobacteriales

"Crocinitomicaceae"

Flavobacteriaceae

Bacteroidales

Rikenellaceae

Marinifilaceae

Marinilabiliaceae 2

Prolixibacteraceae

Alkaliflexus imshenetskii

Marinilabiliaceae 1

Marinilabiliaceae 3 [incl. Cytophaga xylanolytica]

Odoribacteraceae

Porphyromonadaceae

Bacteroidaceae

Taxonomy[edit] 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
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
Bacteroidetes
Order III. Incertae sedis; incl. Flexibacter species group 2]

Class Sphingobacteria
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
Flavobacteriia
Bernardet 2012

Order Flavobacteriales
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
Flavobacteriaceae
Reichenbach et al. 1992 emend. Bernardet et al. 2002

Class Bacteroidia Krieg 2012

Order Bacteroidales
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
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[edit]

^ 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. doi:10.1016/j.ajog.2015.06.039. ISSN 0002-9378. PMID 26428492.  ^ 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
Bacteroidetes
and Chlorobi
Chlorobi
species". BMC Evolutionary Biology. 7: 71. doi:10.1186/1471-2148-7-71. PMC 1887533 . PMID 17488508.  ^ a b c Gupta, R. S. (2004). "The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes". Critical Reviews in Microbiology. 30 (2): 123–140. doi:10.1080/10408410490435133. PMID 15239383.  ^ 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 (Pt 9): 2611–22. doi:10.1099/00221287-147-9-2611. PMID 11535801.  ^ '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[edit]

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

v t e

Prokaryotes: Bacteria
Bacteria
classification (phyla and orders)

Domain Archaea Bacteria Eukaryota (Supergroup Plant Hacrobia Heterokont Alveolata Rhizaria Excavata Amoebozoa Opisthokonta

Animal Fungi)

G-/ OM

Terra-/ Glidobacteria (BV1)

Eobacteria

Deinococcus–Thermus

Deinococcales Thermales

Chloroflexi

Anaerolineales Caldilineales Chloroflexales Herpetosiphonales Dehalococcoidales Ktedonobacterales Thermogemmatisporales Thermomicrobiales Sphaerobacterales

other glidobacteria

Thermodesulfobacteria thermophiles

Aquificae Thermotogae

Cyanobacteria

Proteobacteria (BV2)

Alpha

Caulobacterales Kiloniellales Kordiimonadales Magnetococcales Parvularculales Rhizobiales Rhodobacterales Rhodospirillales Rickettsiales Sneathiellales Sphingomonadales

Beta

Burkholderiales Hydrogenophilales Methylophilales Neisseriales Nitrosomonadales Procabacteriales Rhodocyclales

Gamma

Acidithiobacillales Aeromonadales Alteromonadales Cardiobacteriales Chromatiales Enterobacteriales Legionellales Methylococcales Oceanospirillales Orbales Pasteurellales Pseudomonadales Salinisphaerales Thiotrichales Vibrionales Xanthomonadales

Delta

Bdellovibrionales Desulfarculales Desulfobacterales Desulfovibrionales Desulfurellales Desulfuromonadales Myxococcales Syntrophobacterales Syntrophorhabdales

Epsilon

Campylobacterales Nautiliales

Zeta

Mariprofundales

BV4

Spirochaetes

Spirochaetes

Sphingobacteria (FCB group)

Fibrobacteres Chlorobi

Chlorobiales Ignavibacteriales

Bacteroidetes

Bacteroidales Cytophagales Flavobacteriales Sphingobacteriales

Planctobacteria/ (PVC group)

Chlamydiae Lentisphaerae

Lentisphaerales Oligosphaerales Victivallales

Planctomycetes

Phycisphaerales Planctomycetales

Verrucomicrobia

Puniceicoccales Opitutales Chthoniobacterales Verrucomicrobiales

"Poribacteria"

Other GN

Acidobacteria

Acidobacteriales Acanthopleuribacterales Holophagales Solibacterales

Armatimonadetes

Armatimonadales Chthonomonadales Fimbriimonadales

Caldiserica Chrysiogenetes Deferribacteres Dictyoglomi Elusimicrobia Fusobacteria Gemmatimonadetes Nitrospirae Synergistetes

G+/ no OM

Firmicutes (BV3)

Bacilli

Bacillales Lactobacillales

Clostridia

Clostridiales Halanaerobiales Thermoanaerobacteriales Natranaerobiales

Erysipelotrichia

Erysipelotrichiales

Thermolithobacteria

Thermolithobacterales

Tenericutes/ Mollicutes

Mycoplasmatales Entomoplasmatales Anaeroplasmatales Acholeplasmatales Haloplasmatales

Negativicutes

Selenomonadales

Actinobacteria (BV5)

Actinobacteria

Actinomycetales Bifidobacteriales

Acidimicrobiia

Acidimicrobiales

Coriobacteriidae

Coriobacteriales

Nitriliruptoria

Euzebyales Nitriliruptorales

Rubrobacteria

Gaiellales Rubrobacterales Thermoleophilales Solirubrobacterales

Incertae sedis

†Archaeosphaeroides †Eobacterium †Leptotrichites

Source: Bergey's Manual (2001–2012). Alternative views: Wikispecies.

v t e

Infectious diseases Bacterial diseases: BV4 non-proteobacterial G- (primarily A00–A79, 001–041, 080–109)

Spirochaete

Spirochaetaceae

Treponema

Treponema
Treponema
pallidum

Syphilis/bejel Yaws

Treponema
Treponema
carateum (Pinta) Treponema
Treponema
denticola

Borrelia

Borrelia
Borrelia
burgdorferi/ Borrelia
Borrelia
afzelii

Lyme disease Erythema chronicum migrans Neuroborreliosis

Borrelia
Borrelia
recurrentis (Louse borne relapsing fever) Borrelia
Borrelia
hermsii/ Borrelia
Borrelia
duttoni/ Borrelia
Borrelia
parkeri (Tick borne relapsing fever)

Leptospiraceae

Leptospira

Leptospira
Leptospira
interrogans (Leptospirosis)

Chlamydiaceae

Chlamydophila

Chlamydophila psittaci (Psittacosis) Chlamydophila pneumoniae

Chlamydia

Chlamydia trachomatis

Chlamydia Lymphogranuloma venereum Trachoma

Bacteroidetes

Bacteroides
Bacteroides
fragilis Tannerella forsythia Capnocytophaga canimorsus Porphyromonas gingivalis Prevotella intermedia

Fusobacteria

Fusobacterium necrophorum (Lemierre's syndrome) Fusobacterium nucleatum Fusobacterium polymorphum

Streptobacillus moniliformis (Rat-bite fever/Haverhill fever)

Biology portal

Taxon identifiers

Wd: Q1061265 EoL: 7835 ITIS

.