Bacteroidota

{{short description|Phylum of Gram-negative bacteria}} {{Automatic taxobox | name = Bacteroidota | image = Bacteroides biacutis 01.jpg | image_alt = Bacteroides biacutis | image_caption = ''Bacteroides biacutis'' | display_parents = 2 | taxon = Bacteroidota | authority = Krieg et al. 2021<ref>{{cite journal | vauthors = Oren A, Garrity GM | title = Valid publication of the names of forty-two phyla of prokaryotes | journal = Int J Syst Evol Microbiol | year = 2021 | volume = 71 | issue = 10 | pages = 5056 | doi = 10.1099/ijsem.0.005056 | pmid = 34694987 | s2cid = 239887308 | doi-access = free }}</ref> | subdivision_ranks = Classes | subdivision_ref = <ref name=LPSN>{{lpsn3|phylum/bacteroidota|Bacteroidota}}</ref><ref name=NCBI>{{cite web |author=Schoch CL |display-authors=et al. |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?command=show&mode=tree&id=976&lvl=3 |title=Bacteroidota |accessdate=2025-06-05 |publisher=National Center for Biotechnology Information (NCBI) taxonomy database}}</ref> | subdivision = * Bacteroidia Krieg 2012 * Chitinophagia Munoz et al. 2017 * Cytophagia Nakagawa 2012 * Flavobacteriia Bernardet 2012 * Saprospiria Hahnke et al. 2018 * Sphingobacteriia Kämpfer 2012 | synonyms = * "Bacteroidaeota" Oren et al. 2015 * "Bacteroidetes" Krieg et al. 2010<ref>{{cite book | vauthors = Krieg NR, Ludwig W, Euzéby J, Whitman WB | chapter = Phylum XIV. ''Bacteroidetes'' phyl. nov. |veditors= Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB | title = Bergey's Manual of Systematic Bacteriology | edition = 2nd | volume = 4 | publisher = Springer | location = New York, NY | year = 2010 | pages = 25}}</ref> * "Bacteroidota" Whitman et al. 2018 * "Saprospirae" Margulis and Schwartz 1998 * "Sphingobacteria" Cavalier-Smith 2002 }}

The phylum '''Bacteroidota''' (synonym '''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.

Although some ''Bacteroides'' spp. can be opportunistic pathogens, many ''Bacteroidota'' 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. ''Bacteroidota'' colonize the gastrointestinal tract already in infants, as non-digestible oligosaccharides in mother milk support the growth of both ''Bacteroides'' and ''Bifidobacterium'' spp. ''Bacteroides'' spp. are selectively recognized by the immune system of the host through specific interactions.<ref name=":0">{{Cite journal|last1=Rajilić-Stojanović|first1=Mirjana|last2=de Vos|first2=Willem M.|date=2014|title=The first 1000 cultured species of the human gastrointestinal microbiota|journal=FEMS Microbiology Reviews|language=en|volume=38|issue=5|pages=996–1047|doi=10.1111/1574-6976.12075|issn=1574-6976|pmc=4262072|pmid=24861948}}</ref>

== History == ''Bacteroides fragilis'' was the first ''Bacteroides'' species isolated in 1898 as a human pathogen linked to appendicitis among other clinical cases.<ref name=":0" /> By far, the species in the class ''Bacteroidia'' 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 {{clarify-span|fourth volume|reason=Shouldn't this say "second edition"? Or did Volumes 1 to 3 of the second edition still refer to Bacteroidetes? If so, then it should read "fourth volume of the second edition". In any case, this is all a bit of a roundabout way of referring to the year of the change! —DIV|date=February 2024}} of Bergey's ''Manual of Systematic Bacteriology''.<ref>{{cite book|url=https://www.springer.com/life+sciences/book/978-0-387-95042-6|title=The ''Bacteroidetes'', ''Spirochaetes'', ''Tenericutes'' (''Mollicutes''), ''Acidobacteria'', ''Fibrobacteres'', ''Fusobacteria'', ''Dictyoglomi'', ''Gemmatimonadetes'', ''Lentisphaerae'', ''Verrucomicrobia'', ''Chlamydiae'', and ''Planctomycetes''|author=Krieg, N.R.|author2=Ludwig, W.|author3=Whitman, W.B.|author4=Hedlund, B.P.|author5=Paster, B.J.|author6=Staley, J.T.|author7=Ward, N.|author8=Brown, D.|author9=Parte, A.|date=November 24, 2010|publisher=Springer|isbn=978-0-387-95042-6|editor=George M. Garrity|edition=2nd|series=Bergey's Manual of Systematic Bacteriology|volume=4|location=New York|pages=908|id=British Library no. GBA561951|orig-year=1984(Williams & Wilkins)}}</ref>

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 species of ''Bacteroides'' have undergone reclassification. Based on current classification, the majority of the gastrointestinal ''Bacteroidota'' species belong to the families ''Bacteroidaceae'', ''Prevotellaceae'', ''Rikenellaceae'', and ''Porphyromonadaceae''. <ref name=":0" /> This phylum is sometimes grouped with ''Chlorobiota'', ''Fibrobacterota'', ''Gemmatimonadota'', ''Calditrichota'', and marine group A to form the FCB group or superphylum.<ref name="Gupta">{{cite journal|last1=Gupta|first1=R. S.|last2=Lorenzini|first2=E.|year=2007|title=Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species|journal=BMC Evolutionary Biology|volume=7|issue=1 |page=71|doi=10.1186/1471-2148-7-71|pmc=1887533|pmid=17488508 |doi-access=free |bibcode=2007BMCEE...7...71G }}</ref> In the alternative classification system proposed by Cavalier-Smith, this taxon is instead a class in the phylum Sphingobacteria.

== Medical and ecological role == In the gastrointestinal microbiota ''Bacteroidota'' have a very broad metabolic potential and are regarded as one of the most stable part of gastrointestinal microflora. Reduced abundance of the ''Bacteroidota'' in some cases is associated with obesity. This bacterial group as a whole has conflicting evidence for alteration of abundance in patients with irritable bowel syndrome, though its genus ''Bacteroides'' is likely enriched,<ref>{{cite journal|vauthors=Pittayanon R, Lau JT, Yuan Y, Leontiadis GI, Tse F, Surette M, Moayyedi P|title=Gut Microbiota in Patients With Irritable Bowel Syndrome-A Systematic Review|journal=Gastroenterology|year=2019|volume=157|issue=1|pages=97–108|doi=10.1053/j.gastro.2019.03.049|pmid=30940523}}</ref> but it may be involved in type 1 and type 2 diabetes pathogenesis.<ref name=":0" /> ''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. ''Bacteroidota'' species that belong to classes ''Flavobacteriales'' and ''Sphingobacteriales'' are typical soil bacteria and are only occasionally detected in the gastrointestinal tract, except ''Capnocytophaga spp.'' and ''Sphingobacterium spp.'' that can be detected in the human oral cavity.<ref name=":0" />

''Bacteroidota'' are not limited to gut microbiota, they colonize a variety of habitats on Earth.<ref name=":1">{{Cite journal|last1=Thomas|first1=François|last2=Hehemann|first2=Jan-Hendrik|last3=Rebuffet|first3=Etienne|last4=Czjzek|first4=Mirjam|last5=Michel|first5=Gurvan|date=2011|title=Environmental and Gut ''Bacteroidetes'': The Food Connection|journal=Frontiers in Microbiology|volume=2|pages=93|doi=10.3389/fmicb.2011.00093|issn=1664-302X|pmc=3129010|pmid=21747801|doi-access=free }}</ref> For example, ''Bacteroidota'', together with "Pseudomonadota", "Bacillota", and "Actinomycetota", are also among the most abundant bacterial groups in rhizosphere.<ref>{{Cite journal|last1=Mendes|first1=Rodrigo|last2=Garbeva|first2=Paolina|last3=Raaijmakers|first3=Jos M.|date=2013|title=The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms|journal=FEMS Microbiology Reviews|language=en|volume=37|issue=5|pages=634–663|doi=10.1111/1574-6976.12028|pmid=23790204|issn=1574-6976|doi-access=free}}</ref> They have been detected in soil samples from various locations, including cultivated fields, greenhouse soils and unexploited areas.<ref name=":1" /> ''Bacteroidota'' 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.<ref name=":1" /> Halophilic ''Bacteroidota'' 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.<ref>{{Cite journal|last=Oren|first=Aharon|date=2013|title=''Salinibacter'': An extremely halophilic bacterium with archaeal properties|journal=FEMS Microbiology Letters|language=en|volume=342|issue=1|pages=1–9|doi=10.1111/1574-6968.12094|pmid=23373661|doi-access=free}}</ref>

== Metabolism == Gastrointestinal ''Bacteroidota'' 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 ''Bacteroidota'' 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.<ref name=":0" /> Many members of the ''Bacteroidota'' 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 ''Bacteroidota'' 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.<ref>{{Cite journal|last1=Jehlička|first1=Jan|last2=Osterrothová|first2=Kateřina|last3=Oren|first3=Aharon|last4=Edwards|first4=Howell G. M.|date=2013|title=Raman spectrometric discrimination of flexirubin pigments from two genera of ''Bacteroidetes''|journal=FEMS Microbiology Letters|language=en|volume=348|issue=2|pages=97–102|doi=10.1111/1574-6968.12243|pmid=24033756|doi-access=free}}</ref>

==Genomics== Comparative genomic analysis has led to the identification of 27 proteins which are present in most species of the phylum ''Bacteroidota''. Of these, one protein is found in all sequenced ''Bacteroidota'' 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.<ref name="Gupta"/> Additionally, four proteins have been identified which are present in all ''Bacteroidota'' 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 ''Bacteroidota'' 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 ''Bacteroidota'' phylum except ''S. ruber''. This deletion is also found in one ''Chlorobiota'' 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 ''Bacteroidota''.<ref name="Gupta"/>

===Relatedness of ''Bacteroidota'', ''Chlorobiota'', and ''Fibrobacterota'' phyla=== Species from the ''Bacteroidota'' and ''Chlorobiota'' 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 ''Bacteroidota'' and ''Chlorobiota'' phyla.<ref name="Gupta"/> The sharing of these three proteins is significant because other than them, no proteins from either the ''Bacteroidota'' or ''Chlorobiota'' 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.<ref name="Gupta" /><ref name="GuptaB">{{cite journal | last1 = Gupta | first1 = R. S. | year = 2004 | title = The phylogeny and signature sequences characteristics of ''Fibrobacteres'', ''Chlorobi'', and ''Bacteroidetes'' | journal = Critical Reviews in Microbiology | volume = 30 | issue = 2| pages = 123–140 | doi = 10.1080/10408410490435133 | pmid=15239383| s2cid = 24565648 }}</ref> Additionally, the phylum ''Fibrobacterota'' 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<ref name="GuptaB" /> These phyla also branch in the same position based upon conserved signature indels in a number of important proteins.<ref>{{cite journal | last1 = Griffiths | first1 = E | last2 = Gupta | first2 = RS | year = 2001 | title = 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 | journal = Microbiology | volume = 147 | issue = Pt 9| pages = 2611–22 | doi=10.1099/00221287-147-9-2611 | pmid=11535801| doi-access = free }}</ref> 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.<ref name="Gupta"/><ref name="GuptaB" />

==Phylogeny== The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature<ref name="LPSN"/>

{| class="wikitable" |- ! colspan=1 | Whole-genome based phylogeny<ref name="García-López">{{cite journal |vauthors = García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M | title = Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of ''Bacteroidetes'' | journal = Front Microbiol | year = 2019 | volume = 10 | pages = 2083 | pmid = 31608019 | pmc = 6767994 | doi = 10.3389/fmicb.2019.02083| doi-access = free }}</ref> ! colspan=1 | 16S rRNA based LTP_08_2023<ref name=LTP>{{cite web|title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=20 November 2023}}</ref><ref>{{cite web|title=LTP_all tree in newick format|url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_08_2023.ntree |access-date=20 November 2023}}</ref><ref>{{cite web|title=LTP_08_2023 Release Notes| url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_08_2023_release_notes.pdf |access-date=20 November 2023}}</ref> ! colspan=1 | 120 single copy marker proteins based GTDB 10-RS226<ref name="about">{{cite web |title=GTDB release 10-RS226 |url=https://gtdb.ecogenomic.org/about#4%7C |website=Genome Taxonomy Database|access-date=1 May 2025}}</ref><ref name="tree_bac">{{cite web |title=bac120_r226.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release226/226.0/auxillary_files/bac120_r226.sp_labels.tree |website=Genome Taxonomy Database|access-date=1 May 2025}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=Genome Taxonomy Database|access-date=1 May 2025}}</ref> |- | style="vertical-align:top| {{Clade | style=font-size:90%;line-height:80% |1={{clade |1={{clade |1=Chlorobiota |2={{clade |1=Balneolota |2=Rhodothermota }} }} |2={{clade |label1=Bacteroidota |1={{clade |1=Saprospiria |2={{clade |1={{clade |1={{clade |1=Chitinophagia |2=Sphingobacteriia }} |2=Cytophagia }} |2={{clade |1=Bacteroidia |2=Flavobacteriia }} }} }} }} }} }} | {{Clade | style=font-size:90%;line-height:80% |1={{clade |1={{clade |label1=Ignavibacteriota |1=Ignavibacteria |label2=Chlorobiota |2=Chlorobiia }} |2={{clade |1={{clade |label1=Rhodothermota |1=Rhodothermia }} |2={{clade |label1=Balneolota |1=Balneolia |label2=Bacteroidota |2={{clade |1=Raineyaceae |2={{clade |1=Microscillaceae |2={{clade |1={{clade |label1=Cytophagia |1=Cytophagales }} |2={{clade |1={{clade |label1=Chitinophagia |1={{clade |1=Saprospirales |2=Chitinophagales }} }} |2={{clade |1={{clade |label1=Sphingobacteriia |1=Sphingobacteriales }} |2={{clade |label1=Bacteroidia |1=Bacteroidales |label2=Flavobacteriia |2=Flavobacteriales }} }} }} }} }} }} }} }} }} }} | {{Clade | style=font-size:90%;line-height:80% |label1=Bacteroidota_A |1={{clade |1={{clade |1={{clade |label1="Kapabacteria" |1="Kapabacteriales" }} |2={{clade |label1="Kryptonia" |1="Kryptoniales" |label2="Ignavibacteriia" |2={{clade |1="Tepidaquicellales" [SJA-28: 100: B-1AR: Ch128a] |2=Ignavibacteriales }} }} }} |2={{clade |label1=Chlorobiia |1=Chlorobiales |label2=Rhodothermia |2={{clade |1=Balneolales |2=Rhodothermales }} }} }} }} {{Clade | style=font-size:90%;line-height:80% |label1=Bacteroidota |1={{clade |label1=Bacteroidia |1={{clade |1={{clade |1=Blattabacteriaceae {Flavobacteriales_B} |2={{clade |1="Amoebophilaceae" {Cytophagales_A} |2=Cytophagales }} }} |2={{clade |1=Chitinophagales |2={{clade |1=Sphingobacteriales |2={{clade |1={{clade |1=Aurantibacillaceae {B-17B0} |2=Bacteroidales }} |2=Flavobacteriales }} }} }} }} }} }} |}

==References==  {{Reflist}}

==External links== * [http://www.bacterialphylogeny.info/groupspecific/fbc/fbc.html Phylogenomics and Evolutionary Studies on Bacteriodetes, Chlorobi and Fibrobacteres Species] {{Webarchive|url=https://web.archive.org/web/20190322190353/http://www.bacterialphylogeny.info/groupspecific/fbc/fbc.html |date=2019-03-22 }} Bacterial (Prokaryotic) Phylogeny Webpage

Category:Bacteroidota Category:Bacteria phyla Category:Gram-negative bacteria