Bacteroidetes

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
Bacteroides biacutis
Scientific classification
Domain: Bacteria
(unranked): FCB group
(unranked): Bacteroidetes-Chlorobi group
Phylum: Bacteroidetes
Krieg et al. 2012
Classes
Synonyms
  • Bacteroidaeota Oren et al. 2015
  • Rhodothermaeota Munoz, Rossello-Mora & Amann 2016
  • Saprospirae

Although some Bacteroides spp. can be opportunistic pathogens, many Bacteroidetes are symbiotic species highly adjusted to the gastrointestinal tract. Bacteroides are highly abundant in intestines, reaching up to 1011 cells g−1 of intestinal material. They perform metabolic conversions that are essential for the host, such as degradation of proteins or complex sugar polymers. Bacteroidetes colonize the gastrointestinal already in infants, as non-digestible oligosaccharides in mother milk support the growth of both Bacteroides and Bifidobacterium spp. Bacteroides spp., is selectively recognized by the immune system of the host through specific interactions.[1]

History

Bacteroides fragilis was the first Bacteroides species isolated in 1898 as a human pathogen linked to appendicitis among other clinical cases.[1] 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.[2]

For a long time, it was thought that the majority of Gram-negative gastrointestinal tract bacteria belonged to the genus Bacteroides, but in recent years many Bacteroides spp. underwent reclassification. Based on current classification, the majority of the gastrointestinal Bacteroidetes spp. belongs to Bacteroidaceae, Prevotellaceae, Rikenellaceae, and Porphyromonadaceae families.  [1] This phylum is sometimes grouped with Chlorobi, Fibrobacteres, Gemmatimonadates, Caldithrix, and marine group A to form the FCB group or superphylum.[3] In the alternative classification system proposed by Cavalier-Smith, this taxon is instead a class in the Sphingobacteria phylum.

Medical and ecological role

In the gastrointestinal microbiota Bacteroidetes have a very broad metabolic potential and are regarded as one of the most stable part of gastrointestinal microflora. Reduced abundance of the Bacteroidetes in some cases is associated with obesity. This bacterial group appears to be enriched in patients suffering from irritable bowel syndrome[4] and involved in type 1 and type 2 diabetes.[1] Bacteroides spp. in contrast to Prevotella spp. were recently found to be enriched in the metagenomes of subjects with low gene richness that were associated with adiposity, insulin resistance and dyslipidaemia as well as an inflammatory phenotype. Bacteroidetes species that belong to classes Flavobacteriales and Sphingobacteriales are typical soil bacteria and can only occasionally detected in the gastrointestinal tract, except Capnocytophaga spp. and Sphingobacterium spp. that can be detected in the human oral cavity.[1]

Bacteroidetes are not limited to gut microbiota, they colonize a variety of habitats on Earth.[5] For example, Bacteroidetes, together with Proteobacteria, Firmicutes and Actinobacteria, are also among the most abundant bacterial groups in rhizosphere.[6] They have been detected in soil samples from various locations, including cultivated fields, greenhouse soils and unexploited areas.[5] Bacteroidetes also inhabit freshwater lakes, rivers, as well as oceans. They are increasingly recognized as an important compartment of the bacterioplankton in marine environments, especially in pelagic oceans.[5] Halophilic Bacteroidetes genus Salinibacter inhabit hypersaline environments such as salt-saturated brines in hypersaline lakes. Salinibacter  shares many properties with halophilic Archaea such as Halobacterium and Haloquadratum that inhabit the same environments. Phenotypically, Salinibacter is remarkably similar to Halobacterium and therefore for a long time remained unidentified.[7]

Metabolism

Gastrointestinal Bacteroidetes species produce succinic acid, acetic acid, and in some cases propionic acid, as the major end-products. Species belonging to the genera Alistipes, Bacteroides, Parabacteroides, Prevotella, Paraprevotella, Alloprevotella, Barnesiella, and Tannerella are saccharolytic, while species belonging to Odoribacter and Porphyromonas are predominantly asaccharolytic. Some Bacteroides spp. and Prevotella spp. can degrade complex plant polysaccharides such as starch, cellulose, xylans, and pectins. The Bacteroidetes species also play an important role in protein metabolism by proteolytic activity assigned to the proteases linked to the cell. Some Bacteroides spp. have a potential to utilize urea as a nitrogen source. Other important functions of Bacteroides spp. include the deconjugation of bile acids and growth on mucus.[1] Many members of the Bacteroidetes genera (Flexibacter, Cytophaga, Sporocytophaga and relatives) are coloured yellow-orange to pink-red due to the presence of pigments of the flexirubin group. In some Bacteroidetes strains, flexirubins may be present together with carotenoid pigments. Carotenoid pigments are usually found in marine and halophilic members of the group, whereas flexirubin pigments are more frequent in clinical, freshwater or soil-colonizing representatives.[8]

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.[3] 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.[3]

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.[3] 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.[3][9] 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[9] These phyla also branch in the same position based upon conserved signature indels in a number of important proteins.[10] 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.[3][9]

Phylogeny

The phylogeny is based on 16S rRNA-based LTP release 123 by 'The All-Species Living Tree' Project.[11]

 
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

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[12] and National Center for Biotechnology Information (NCBI).[13]

  • Genus ?"Bifissio" ♠ 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
  • Class "Chitinophagia" Munoz, Rossello-Mora & Amann 2016
  • 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

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. Rajilić-Stojanović, Mirjana; de Vos, Willem M. (2014). "The first 1000 cultured species of the human gastrointestinal microbiota". FEMS Microbiology Reviews. 38 (5): 996–1047. doi:10.1111/1574-6976.12075. ISSN 1574-6976. PMC 4262072. PMID 24861948.
  2. 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.
  3. 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. PMC 1887533. PMID 17488508.
  4. Pittayanon R. et al., Gastroenterology, 2019, 157(1):97-108.
  5. Thomas, François; Hehemann, Jan-Hendrik; Rebuffet, Etienne; Czjzek, Mirjam; Michel, Gurvan (2011). "Environmental and Gut Bacteroidetes: The Food Connection". Frontiers in Microbiology. 2: 93. doi:10.3389/fmicb.2011.00093. ISSN 1664-302X. PMC 3129010. PMID 21747801.
  6. Mendes, Rodrigo; Garbeva, Paolina; Raaijmakers, Jos M. (2013). "The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms". FEMS Microbiology Reviews. 37 (5): 634–663. doi:10.1111/1574-6976.12028. ISSN 1574-6976. PMID 23790204.
  7. Oren, Aharon (2013). "Salinibacter : an extremely halophilic bacterium with archaeal properties". FEMS Microbiology Letters. 342 (1): 1–9. doi:10.1111/1574-6968.12094. PMID 23373661.
  8. Jehlička, Jan; Osterrothová, Kateřina; Oren, Aharon; Edwards, Howell G. M. (2013). "Raman spectrometric discrimination of flexirubin pigments from two genera of Bacteroidetes". FEMS Microbiology Letters. 348 (2): 97–102. doi:10.1111/1574-6968.12243. PMID 24033756.
  9. 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. S2CID 24565648.
  10. 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.
  11. 'The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.
  12. J.P. Euzéby. "Bacteroidetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
  13. Sayers; et al. "Bacteroidetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.
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