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nyms bacteroidaeota oren et al 2015 bacteroidetes krieg et al 2010 4 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 10 11 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 5 history edit bacteroides fragilis was the first bacteroides species isolated in 1898 as a human pathogen linked to appendicitis among other clinical cases 5 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 fourth volume clarification needed of bergey s manual of systematic bacteriology 6 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 5 this phylum is sometimes grouped with chlorobiota fibrobacterota gemmatimonadota calditrichota and marine group a to form the fcb group or superphylum 7 in the alternative classification system proposed by cavalier smith this taxon is instead a class in the phylum sphingobacteria medical and ecological role edit 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 8 but it may be involved in type 1 and type 2 diabetes pathogenesis 5 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 5 bacteroidota are not limited to gut microbiota they colonize a variety of habitats on earth 9 for example bacteroidota together with pseudomonadota bacillota and actinomycetota are also among the most abundant bacterial groups in rhizosphere 10 they have been detected in soil samples from various locations including cultivated fields greenhouse soils and unexploited areas 9 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 9 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 11 metabolism edit 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 5 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 12 genomics edit 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 7 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 7 relatedness of bacteroidota chlorobiota and fibrobacterota phyla edit 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 7 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 7 13 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 13 these phyla also branch in the same position based upon conserved signature indels in a number of important proteins 14 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 7 13 phylogeny edit the currently accepted taxonomy is based on the list of prokaryotic names with standing in nomenclature 2 whole genome based phylogeny 15 16s rrna based ltp _08_2023 16 17 18 120 single copy marker proteins based gtdb 10 rs226 19 20 21 chlorobiota balneolota rhodothermota bacteroidota saprospiria chitinophagia sphingobacteriia cytophagia bacteroidia flavobacteriia ignavibacteriota ignavibacteria chlorobiota chlorobiia rhodothermota rhodothermia balneolota balneolia bacteroidota raineyaceae microscillaceae cytophagia cytophagales chitinophagia saprospirales chitinophagales sphingobacteriia sphingobacteriales bacteroidia bacteroidales flavobacteriia flavobacteriales bacteroidota_a kapabacteria kapabacteriales kryptonia kryptoniales ignavibacteriia tepidaquicellales sja 28 100 b 1ar ch128a ignavibacteriales chlorobiia chlorobiales rhodothermia balneolales rhodothermales bacteroidota bacteroidia blattabacteriaceae flavobacteriales_b amoebophilaceae cytophagales_a cytophagales chitinophagales sphingobacteriales aurantibacillaceae b 17b0 bacteroidales flavobacteriales see also edit list of bacteria genera list of bacterial orders references edit 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 pmid 34694987 s2cid 239887308 1 2 bacteroidota in lpsn freese h m meier kolthoff j p sardà carbasse j afolayan a o göker m 2026 tygs and lpsn in 2025 a global core biodata resource for genome based classification and nomenclature of prokaryotes within dsmz digital diversity nucleic acids research 54 d1 d884 d891 doi 10 1093 nar gkaf1110 schoch cl et al bacteroidota national center for biotechnology information ncbi taxonomy database retrieved 2025 06 05 krieg nr ludwig w euzéby j whitman wb 2010 phylum xiv bacteroidetes phyl 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 1 2 3 4 5 6 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 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 vol 4 2nd ed new york springer p 908 isbn 978 0 387 95042 6 british library no gba561951 1 2 3 4 5 6 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 1 71 bibcode 2007bmcee 7 71g doi 10 1186 1471 2148 7 71 pmc 1887533 pmid 17488508 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 pmid 30940523 1 2 3 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 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 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 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 1 2 3 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 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 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 of bacteroidetes front microbiol 10 2083 doi 10 3389 fmicb 2019 02083 pmc 6767994 pmid 31608019 the ltp retrieved 20 november 2023 ltp_all tree in newick format retrieved 20 november 2023 ltp_08_2023 release notes pdf retrieved 20 november 2023 gtdb release 10 rs226 genome taxonomy database retrieved 1 may 2025 bac120_r226 sp_label genome taxonomy database retrieved 1 may 2025 taxon history genome taxonomy database retrieved 1 may 2025 external links edit phylogenomics and evolutionary studies on bacteriodetes chlorobi and fibrobacteres species archived 2019 03 22 at the wayback machine bacterial prokaryotic phylogeny webpage v t e prokaryotes bacteria classification domain archaea bacteria eukaryota major groups metamonada discoba diaphoretickes hacrobia cryptista rhizaria alveolata stramenopiles plants amorphea amoebozoa opisthokonta animalia fungi mesomycetozoea candidate phyla radiation elulimicrobiota elulimicrobia minisyncoccota absconditibacteria andersenbacteria berkelbacteria baikalibacteria dojkabacteriia doudnabacteria gracilibacteriia howlettbacteria katanibacteriia kazanbacteria microgenomatia minisyncoccia patescibacteriia saccharimonadia torokbacteria wirthbacteria thermotogati bipolaricaulota acetithermia bipolaricaulia deinococcota deinococcia synergistetes atribacterota atribacteria phoenicimicrobiia synergistota synergistia thermocalda caldisericota caldisericia coprothermobacterota coprothermobacteria dictyoglomerota...
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