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Bacteroidota

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Bacteroidota
Bacteroides biacutis
Bacteroides biacutis
Scientific classificationEdit this classification
Domain: Bacteria
Clade: FCB group
(unranked): Bacteroidetes-Chlorobi group
Phylum: Bacteroidota
Krieg et al. 2021[1]
Classes[2]
Synonyms
  • "Bacteroidaeota"Oren et al. 2015
  • "Bacteroidetes"Krieg et al. 2010[3]
  • "Bacteroidota"Whitman et al. 2018
  • "Saprospirae"Margulis and Schwartz 1998
  • "Sphingobacteria"Cavalier-Smith 2002

ThephylumBacteroidota(synonymBacteroidetes) is composed of three large classes ofGram-negative,nonsporeforming, anaerobic or aerobic, and rod-shapedbacteriathat 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.

Although someBacteroidesspp. can beopportunistic pathogens,manyBacteroidotaaresymbiotic specieshighly adjusted to the gastrointestinal tract.Bacteroidesare highly abundant in intestines, reaching up to 1011cells g−1of intestinal material. They perform metabolic conversions that are essential for the host, such as degradation of proteins or complex sugar polymers.Bacteroidotacolonize the gastrointestinal tract already in infants, as non-digestibleoligosaccharides in mother milksupport the growth of bothBacteroidesandBifidobacteriumspp.Bacteroidesspp. are selectively recognized by theimmune systemof the host through specific interactions.[4]

History

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Bacteroides fragiliswas the firstBacteroidesspecies isolated in 1898 as a human pathogen linked toappendicitisamong other clinical cases.[4]By far, the species in theclassBacteroidiaare the most well-studied, including the genusBacteroides(an abundant organism in thefecesof warm-blooded animals including humans), andPorphyromonas,a group of organisms inhabiting the humanoral cavity.The classBacteroidiawas formerly calledBacteroidetes;as it was until recently the only class in the phylum, the name was changed in thefourth volume[clarify]of Bergey'sManual of Systematic Bacteriology.[5]

For a long time, it was thought that the majority of Gram-negative gastrointestinal tract bacteria belonged to the genusBacteroides,but in recent years many species ofBacteroideshave undergone reclassification. Based on current classification, the majority of the gastrointestinalBacteroidotaspecies belong to the familiesBacteroidaceae,Prevotellaceae,Rikenellaceae,andPorphyromonadaceae.[4] This phylum is sometimes grouped withChlorobiota,Fibrobacterota,Gemmatimonadota,Calditrichota,andmarine group Ato form theFCB groupor superphylum.[6]In the alternative classification system proposed byCavalier-Smith,this taxon is instead a class in the phylumSphingobacteria.

Medical and ecological role

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In the gastrointestinalmicrobiotaBacteroidotahave a very broad metabolic potential and are regarded as one of the most stable part of gastrointestinal microflora. Reduced abundance of theBacteroidotain some cases is associated withobesity.This bacterial group as a whole has conflicting evidence for alteration of abundance in patients withirritable bowel syndrome,though its genusBacteroidesis likely enriched,[7]but it may be involved intype 1andtype 2 diabetespathogenesis.[4]Bacteroidesspp. in contrast toPrevotellaspp. 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.Bacteroidotaspecies that belong to classesFlavobacterialesandSphingobacterialesare typical soil bacteria and are only occasionally detected in the gastrointestinal tract, exceptCapnocytophagaspp.andSphingobacteriumspp.that can be detected in the human oral cavity.[4]

Bacteroidotaare not limited to gut microbiota, they colonize a variety of habitats on Earth.[8]For example,Bacteroidota,together with "Pseudomonadota","Bacillota",and"Actinomycetota",are also among the most abundant bacterial groups inrhizosphere.[9]They have been detected in soil samples from various locations, including cultivated fields, greenhouse soils and unexploited areas.[8]Bacteroidotaalso inhabit freshwater lakes, rivers, as well as oceans. They are increasingly recognized as an important compartment of thebacterioplanktonin marine environments, especially inpelagic oceans.[8]HalophilicBacteroidotagenusSalinibacterinhabit hypersaline environments such as salt-saturated brines in hypersaline lakes.Salinibactershares many properties with halophilicArchaeasuch asHalobacteriumandHaloquadratumthat inhabit the same environments. Phenotypically,Salinibacteris remarkably similar toHalobacteriumand therefore for a long time remained unidentified.[10]

Metabolism

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GastrointestinalBacteroidotaspecies producesuccinic acid,acetic acid,and in some casespropionic acid,as the major end-products. Species belonging to the generaAlistipes,Bacteroides,Parabacteroides,Prevotella,Paraprevotella,Alloprevotella,Barnesiella,andTannerellaare saccharolytic, while species belonging toOdoribacterandPorphyromonasare predominantly asaccharolytic. SomeBacteroides spp.andPrevotella spp.can degrade complex plant polysaccharides such asstarch,cellulose,xylans,andpectins.TheBacteroidotaspecies also play an important role in protein metabolism by proteolytic activity assigned to theproteaseslinked to the cell. Some "Bacteroidesspp. have a potential to utilizeureaas a nitrogen source. Other important functions ofBacteroidesspp. include the deconjugation ofbile acidsand growth onmucus.[4]Many members of theBacteroidotagenera (Flexibacter,Cytophaga,Sporocytophagaand relatives) are coloured yellow-orange to pink-red due to the presence of pigments of theflexirubingroup. In someBacteroidotastrains, flexirubins may be present together withcarotenoidpigments. Carotenoid pigments are usually found in marine andhalophilicmembers of the group, whereas flexirubin pigments are more frequent in clinical, freshwater or soil-colonizing representatives.[11]

Genomics

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Comparative genomic analysis has led to the identification of 27 proteins which are present in most species of the phylumBacteroidota.Of these, one protein is found in all sequencedBacteroidotaspecies, while two other proteins are found in all sequenced species with the exception of those from the genusBacteroides.The absence of these two proteins in this genus is likely due to selective gene loss.[6]Additionally, four proteins have been identified which are present in allBacteroidotaspecies exceptCytophaga hutchinsonii;this is again likely due to selective gene loss. A further eight proteins have been identified which are present in all sequencedBacteroidotagenomes exceptSalinibacter ruber.The absence of these proteins may be due to selective gene loss, or becauseS. ruberbranches very deeply, the genes for these proteins may have evolved after the divergence ofS. ruber.Aconserved signature indelhas also been identified; this three-amino-acid deletion in ClpBchaperoneis present in all species of theBacteroidotaphylum exceptS. ruber.This deletion is also found in oneChlorobiotaspecies and oneArchaeumspecies, which is likely due tohorizontal gene transfer.These 27 proteins and the three-amino-acid deletion serve as molecular markers for theBacteroidota.[6]

Relatedness ofBacteroidota,Chlorobiota,andFibrobacterotaphyla

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Species from theBacteroidotaandChlorobiotaphyla 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 theBacteroidotaandChlorobiotaphyla.[6]The sharing of these three proteins is significant because other than them, no proteins from either theBacteroidotaorChlorobiotaphyla 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.[6][12]Additionally, the phylumFibrobacterotais 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[12]These phyla also branch in the same position based upon conserved signature indels in a number of important proteins.[13]Lastly and most importantly, two conserved signature indels (in the RpoC protein and inserine 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.[6][12]

Phylogeny

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The currently accepted taxonomy is based on theList of Prokaryotic names with Standing in Nomenclature[2]

Whole-genome based phylogeny[14] 16S rRNA basedLTP_08_2023[15][16][17] 120 single copy marker proteins basedGTDB08-RS214[18][19][20]
Bacteroidota

See also

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References

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  1. ^Oren A, Garrity GM (2021)."Valid publication of the names of forty-two phyla of prokaryotes".Int J Syst Evol Microbiol.71(10): 5056.doi:10.1099/ijsem.0.005056.PMID34694987.S2CID239887308.
  2. ^abEuzéby JP, Parte AC.""Bacteroidetes"".List of Prokaryotic names with Standing in Nomenclature(LPSN).RetrievedJune 23,2021.
  3. ^Krieg NR, Ludwig W, Euzéby J, Whitman WB (2010). "Phylum XIV.Bacteroidetesphyl. nov. ". In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds.).Bergey's Manual of Systematic Bacteriology.Vol. 4 (2nd ed.). New York, NY: Springer. p. 25.
  4. ^abcdefRajilić-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.ISSN1574-6976.PMC4262072.PMID24861948.
  5. ^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.).TheBacteroidetes,Spirochaetes,Tenericutes(Mollicutes),Acidobacteria,Fibrobacteres,Fusobacteria,Dictyoglomi,Gemmatimonadetes,Lentisphaerae,Verrucomicrobia,Chlamydiae,andPlanctomycetes.Bergey's Manual of Systematic Bacteriology. Vol. 4 (2nd ed.). New York: Springer. p. 908.ISBN978-0-387-95042-6.British Library no. GBA561951.
  6. ^abcdefGupta, 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(1): 71.Bibcode:2007BMCEE...7...71G.doi:10.1186/1471-2148-7-71.PMC1887533.PMID17488508.
  7. ^Pittayanon R, Lau JT, Yuan Y, Leontiadis GI, Tse F, Surette M, Moayyedi P (2019). "Gut Microbiota in Patients With Irritable Bowel Syndrome-A Systematic Review".Gastroenterology.157(1): 97–108.doi:10.1053/j.gastro.2019.03.049.PMID30940523.
  8. ^abcThomas, François; Hehemann, Jan-Hendrik; Rebuffet, Etienne; Czjzek, Mirjam; Michel, Gurvan (2011)."Environmental and GutBacteroidetes:The Food Connection ".Frontiers in Microbiology.2:93.doi:10.3389/fmicb.2011.00093.ISSN1664-302X.PMC3129010.PMID21747801.
  9. ^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.ISSN1574-6976.PMID23790204.
  10. ^Oren, Aharon (2013)."Salinibacter:An extremely halophilic bacterium with archaeal properties ".FEMS Microbiology Letters.342(1): 1–9.doi:10.1111/1574-6968.12094.PMID23373661.
  11. ^Jehlička, Jan; Osterrothová, Kateřina; Oren, Aharon; Edwards, Howell G. M. (2013)."Raman spectrometric discrimination of flexirubin pigments from two genera ofBacteroidetes".FEMS Microbiology Letters.348(2): 97–102.doi:10.1111/1574-6968.12243.PMID24033756.
  12. ^abcGupta, R. S. (2004). "The phylogeny and signature sequences characteristics ofFibrobacteres,Chlorobi,andBacteroidetes".Critical Reviews in Microbiology.30(2): 123–140.doi:10.1080/10408410490435133.PMID15239383.S2CID24565648.
  13. ^Griffiths, E; Gupta, RS (2001)."The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: Evidence thatFibrobacterdiverged at a similar time toChlamydiaand theCytophaga–Flavobacterium–Bacteroidesdivision ".Microbiology.147(Pt 9): 2611–22.doi:10.1099/00221287-147-9-2611.PMID11535801.
  14. ^García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M (2019)."Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification ofBacteroidetes".Front Microbiol.10:2083.doi:10.3389/fmicb.2019.02083.PMC6767994.PMID31608019.
  15. ^"The LTP".Retrieved20 November2023.
  16. ^"LTP_all tree in newick format".Retrieved20 November2023.
  17. ^"LTP_08_2023 Release Notes"(PDF).Retrieved20 November2023.
  18. ^"GTDB release 08-RS214".Genome Taxonomy Database.Retrieved10 May2023.
  19. ^"bac120_r214.sp_label".Genome Taxonomy Database.Retrieved10 May2023.
  20. ^"Taxon History".Genome Taxonomy Database.Retrieved10 May2023.
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