Bacterial phyla
This article is missing information about 2021 renames with "-ota" suffix due to ICNP update. See NCBI description (has link to the 42 new "validly published" names); analogous 2023 renames of Candidatus phyla in doi:10.1099/ijsem.0.005821. (December 2021) |
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.[2]
It has been estimated that ~1,300 bacterial phyla exist.
The rank of phylum has been included in the rules of the International Code of Nomenclature of Prokaryotes, using the ending –ota for phylum names that must be based on the name of a genus as its nomenclatural type.[7][8]
List of bacterial phyla
The following is a list of bacterial phyla that have been validly published (not current).
Phylum | Alternative names | Group | Cultured representative | Notes |
---|---|---|---|---|
10bav-F6[9] | No | |||
"Abawacabacteria"[4][10] | RIF46 | CPR; Gracilibacteria-related CPR | No | |
"Abditibacteriota"[11] | FBP | Yes[11] | ||
"Absconditabacteria"[12][10] | SR1 | CPR; Gracilibacteria-related CPR | No | |
ABY1[13] | OD1-ABY1[14] | CPR; Parcubacteria | No | |
"Bipolaricaulota"[15] | OP1, "Acetothermia" | |||
Acidobacteriota | "Acidobacteria" | Yes[16] | ||
Actinomycetota | "Actinobacteria" | Terrabacteria | Yes[17] | |
"Adlerbacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 4 | No | ||
"Aerophobota" / "Aerophobetes" | CD12, BHI80-139 | |||
"Amesbacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Andersenbacteria"[4] | RIF9 | CPR; Parcubacteria; Parcubacteria 4-related | No | |
Armatimonadota[15] | "Armatimonadetes", OP10 | Terrabacteria | Yes[19] | |
"Aminicenantes"[15] | OP8 | |||
AncK6[9] | ||||
Apal-E12[9] | ||||
Atribacterota[15] | OP9, JS1 | No | ||
Aquificota | "Aquificae" | |||
"Azambacteria" i[18][10] | CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria | No | split by Anantharaman et al. … | |
"Azambacteria" ii[18][10] | CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria | No | … (Oct 2016) as being polyphyletic | |
Bacteroidota | "Bacteroidetes" | FCB group | Yes | |
Balneolota[20]
|
Yes | |||
Bdellovibrionota | ||||
"Beckwithbacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Berkelbacteria"[21][10] | ACD58 | CPR; Saccharibacteria-related CPR | No | |
BHI80-139[9] | ||||
"Blackburnbacteria"[4] | RIF35 | CPR; Microgenomates | No | |
"Brennerbacteria"[4][10] | RIF18 | CPR; Parcubacteria; Parcubacteria 3 | No | |
"Brownbacteria"[22] | CPR; Parcubacteria; unclassified Parcubacteria | No | ||
"Buchananbacteria"[4][10] | RIF37 | CPR; Parcubacteria; Parcubacteria 1 | No | |
Caldisericota[15]
|
OP5,[23] "Caldiserica" | FCB group | Yes[24] | |
Calditrichota[25]
|
FCB group[26] | |||
"Calescamantes" | EM19 | |||
"Campbellbacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 4 | No | seem to be polyphyletic: two clades | |
Campylobacterota | ||||
Chlamydiota | "Chlamydiae"[27] | PVC group | ||
Chlorobiota
|
"Chlorobi" | FCB group | ||
Chloroflexota | "Chloroflexi" | "Terrabacteria" | ||
Chisholmbacteria[4] | RIF36 | CPR; "Microgenomates" | No | |
Chrysiogenota
|
"Chrysiogenetes" | |||
"Cloacimonetes"[28] | WWE1 | FCB group[26] | ||
"Coatesbacteria"[4] | RIF8 | No | ||
"Collierbacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Colwellbacteria"[4][10] | RIF41 | CPR; Parcubacteria; Parcubacteria 3 | No | |
Coprothermobacterota | ||||
"Curtissbacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
CPR-1[1] | CPR | No | ||
CPR-3[1] | CPR | No | ||
"Cyanobacteria" | Terrabacteria | |||
"Dadabacteria"[29] | No | |||
"Daviesbacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Delphibacteria"[6] | FCB group | No | ||
"Delongbacteria"[4] | RIF26, H-178 | No | ||
Deferribacterota
|
Deferribacteres | |||
Deinococcota | Deinococcus–Thermus | Terrabacteria | ||
"Dependentiae"[30] | TM6 | |||
Dictyoglomota
|
Dictyoglomi[31] | |||
"Dojkabacteria"[10] | WS6 | CPR; Microgenomates-related CPR | ||
"Dormibacteraeota"[32] | AD3 | No | ||
"Doudnabacteria"[18][10] | SM2F11 | CPR; Parcubacteria; Parcubacteria 1-related | No | |
"Edwardsbacteria"[5][4] | RIF29, UBP-2 [33] | No | ||
"Eisenbacteria"[4] | RIF28 | FCB group | No | |
Elusimicrobiota | Elusimicrobia, OP7, Termite Group 1 (TG1)[23] | Yes[34] | ||
"Eremiobacteraeota"[35][32] | WPS-2, Palusbacterota[36] | No | ||
"Falkowbacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 | No | ||
"Fermentibacteria"[37] | Hyd24-12 | No | ||
"Fertabacteria"[6] | CPR; Gracilibacteria-related CPR | No | ||
Fibrobacterota | "Fibrobacteres" | FCB group | ||
"Firestonebacteria"[4] | RIF1 | No | ||
"Fervidibacteria" | OctSpa1-106 | |||
"Fischerbacteria"[4] | RIF25 | No | ||
Bacillota | "Firmicutes" | Terrabacteria | ||
"Fraserbacteria"[4] | RIF31 | No | ||
Fusobacteriota | "Fusobacteria" | |||
Gemmatimonadota | Gemmatimonadetes[38] | FCB group[26] | Yes[38] | |
"Glassbacteria"[4] | RIF5 | No | ||
"Giovannonibacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 4-related | No | ||
"Gottesmanbacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Gracilibacteria"[39][10] | GN02, BD1-5, SN-2 | CPR; Patescibacteria; Gracilibacteria-related CPR | No | |
"Gribaldobacteria"[4][10] | CPR; Parcubacteria; Parcubacteria 2 | No | ||
"Handelsmanbacteria"[4] | RIF27 | No | ||
"Harrisonbacteria"[4][10] | RIF43 | CPR; Parcubacteria; Parcubacteria 3 | No | |
"Howlettbacteria"[10] | CPR; Saccharibacteria-related CPR | No | ||
"Hugbacteria"[22] | CPR; Parcubacteria; unclassified Parcubacteria | No | ||
"Hydrogenedentes" | NKB19 | No | ||
Ignavibacteriota
|
"Ignavibacteria", ZB1 | FCB group | ||
"Jacksonbacteria"[4][10] | RIF38 | CPR; Parcubacteria; Parcubacteria 1 | No | |
"Jorgensenbacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 3 | No | ||
"Kaiserbacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 4 | No | ||
"Katanobacteria"[40][10] | WWE3 | CPR; Microgenomates-related | No | |
"Kazanbacteria"[10][4] | Kazan | CPR; Saccharibacteria-related CPR | No | |
"Kerfeldbacteria"[4][10] | RIF4 | CPR; Parcubacteria; Parcubacteria 1 | No | |
Kiritimatiellota | ||||
"Komeilibacteria"[4][10] | RIF6 | CPR; Parcubacteria; Parcubacteria 1 | No | sometimes misspelled as "Komelilbacteria"[4] |
"Kryptonia"[41] | No | |||
KSB1 | No | |||
"Krumholzibacteriota"[33] | ||||
"Kuenenbacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 | No | ||
"Lambdaproteobacteria"[4] | RIF24 | Proteobacteria | No | |
"Latescibacteria" | WS3 | FCB group[26] | No | |
LCP-89[42] | ||||
Lentisphaerota | "Lentisphaerae", vadinBE97 | PVC group | ||
"Levybacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Lindowbacteria"[4] | RIF2 | CPR; Saccharibacteria-related CPR | No | |
"Liptonbacteria"[4][10] | RIF42 | CPR; Parcubacteria; Parcubacteria 3 | No | |
"Lloydbacteria"[4][10] | RIF45 | CPR; Parcubacteria; Parcubacteria 4 | No | |
"Magasanikbacteria"[18][43][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 | No | ||
"Margulisbacteria"[4] | RIF30 | No | ||
"Marinimicrobia" | SAR406, Marine Group A | FCB group[26] | Yes | |
"Melainabacteria"[44] | No | |||
" Microgenomates"[45]
|
OP11 | CPR; Patescibacteria | No | Superphylum |
"Modulibacteria"[39][46] | KSB3, GN06 | No | ||
"Moranbacteria"[18][10] | OD1-i[18] | CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria | No | |
"Muproteobacteria"[4] | RIF23 | Proteobacteria | No | |
Myxococcota | ||||
NC10[47][13] | No | |||
"Nealsonbacteria"[4][10] | RIF40 | CPR; Parcubacteria; Parcubacteria 2 | No | |
"Niyogibacteria"[4] | RIF11 | CPR; Parcubacteria; Parcubacteria 4-related | No | |
Nitrospinota | "Nitrospinae"[48] | Yes[49][50] | ||
Nitrospirota | "Nitrospirae" | Yes | ||
"Nomurabacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 | No | ||
"Omnitrophica"[15] | OP3 | PVC group | No | |
"Pacebacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Parcubacteria"[12] | OD1 | CPR | No | Superphylum |
"Parcubacteria" 1[10] | CPR; Parcubacteria | No | ||
"Parcubacteria" 2[10] | CPR; Parcubacteria | No | ||
"Parcubacteria" 3[10] | CPR; Parcubacteria | No | ||
"Parcubacteria" 4[10] | CPR; Parcubacteria | No | ||
"Parcunitrobacteria"[51] | CPR; Parcubacteria; unclassified Parcubacteria[52] | No | Superphylum | |
PAUC34f[53] | sponge‐associated unclassified lineage (SAUL) | FCB group | ||
"Peregrinibacteria"[54][55][56][57][10] | PER | CPR; Gracilibacteria-related CPR | No | |
"Peribacteria"[10] | CPR; Gracilibacteria-related CPR | No | ||
Planctomycetota | "Planctomycetes" | PVC group | ||
"Poribacteria"[58] | PVC group | |||
"Portnoybacteria"[4] | RIF22 | CPR; Parcubacteria; Parcubacteria 4-related | No | |
Pseudomonadota | "Proteobacteria" | |||
"Raymondbacteria"[4] | RIF7 | No | ||
Riflebacteria[4] | RIF32 | No | ||
Rhodothermota
|
||||
"Roizmanbacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Rokubacteria"[29] | No | |||
"Ryanbacteria"[4][10] | RIF10 | CPR; Parcubacteria; Parcubacteri 4-related | No | |
"Saccharibacteria"[30][10] | TM7 | CPR; Saccharibacteria-related CPR | Yes | |
"Saltatorellota"[59] | ||||
"Schekmanbacteria"[4] | RIF3 | Proteobacteria | No | |
"Shapirobacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Spechtbacteria"[4][10] | RIF19 | CPR; Parcubacteria; Parcubacteria 2 | No | |
Spirochaetota
|
"Spirochaetes" | |||
"Staskawiczbacteria"[4][10] | RIF20 | CPR; Parcubacteria; Parcubacteria 2 | No | |
"Sumerlaeota"[60][61] | BRC1 | |||
"Sungbacteria"[4][10] | RIF17 | CPR; Parcubacteria; Parcubacteria 4-related | No | |
Synergistota | "Synergistetes" | |||
TA06[62] | No | |||
"Tagabacteria"[4][10] | RIF12 | CPR; Parcubacteria; Parcubacteria 4-related | No | |
"Taylorbacteria"[4][10] | RIF16 | CPR; Parcubacteria; Parcubacteria 4 | No | |
"Tectomicrobia"[63] | ||||
Mycoplasmatota | "Tenericutes" | |||
"Terrybacteria"[4][10] | RIF13 | CPR; Parcubacteria; Parcubacteria 2 | No | |
Thermodesulfobacteriota | "Thermodesulfobacteria" | |||
Thermomicrobiota
|
"Thermomicrobia" | |||
Thermotogota
|
"Thermotogae", OP2, EM3[23] | Yes[64] | ||
"Torokbacteria"[10] | CPR; Parcubacteria; unclssified Parcubacteria | No | ||
UBP-1[5] | No | |||
UBP-3[5] | No | |||
UBP-4[5] | No | |||
UBP-5[5] | No | |||
UBP-6[5] | No | |||
UBP-7[5] | No | |||
UBP-8[5] | No | |||
UBP-9[5] | No | |||
UBP-10[5] | No | |||
UBP-11[5] | No | |||
UBP-12[5] | No | |||
UBP-13[5] | No | |||
UBP-14[5] | No | |||
UBP-15[5] | No | |||
UBP-16[5] | No | |||
UBP-17[5] | No | |||
"Uhrbacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 | No | seem to be polyphyletic: two clades | |
"Veblenbacteria"[4] | RIF39 | CPR; Parcubacteria; Parcubacteria 1-related | No | |
Verrucomicrobiota | "Verrucomicrobia" | PVC group | ||
"Vogelbacteria"[4][10] | RIF14 | CPR; Parcubacteria; Parcubacteria 4 | No | |
"Wallbacteria"[4] | RIF33 | No | ||
"Wildermuthbacteria"[4][10] | RIF21 | CPR; Parcubacteria; Parcubacteria 2 | No | |
"Wirthbacteria"[65] | CPR-related bacteria | No | ||
"Woesebacteria"[18] | CPR; Patescibacteria; Microgenomates | No | ||
"Wolfebacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; Parcubacteria 3 | No | ||
"Woykebacteria"[4][22] | RIF34 | CPR; Microgenomates | No | |
WOR-1[62] | No | |||
WOR-2[62] | No | |||
WOR-3[62] | No | |||
"Yanofskybacteria"[18][10] | CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria | No | ||
"Yonathbacteria"[4][10] | RIF44 | CPR; Parcubacteria; Parcubacteria 4 | No | |
"Zambryskibacteria"[4][10] | RIF15 | CPR; Parcubacteria; Parcubacteria 4 | No | |
ZB2 | OD1-ZB2[14] | CPR; Parcubacteria | No | |
"Zixibacteria"[66] | FCB group | No |
Supergroups
Despite the unclear branching order for most bacterial phyla, several groups of phyla consistently cluster together and are referred to as supergroups or superphyla. In some instances, bacterial clades clearly consistently cluster together but it is unclear what to call the group. For example, the Candidate Phyla Radiation includes the Patescibacteria group which includes Microgenomates group which includes over 11 bacterial phyla.
Candidate phyla radiation (CPR)
The CPR is a descriptive term referring to a massive monophyletic radiation of candidate phyla that exists within the Bacterial domain.[67] It includes two main clades, the Microgenomates and Parcubacteria groups, each containing the eponymous superphyla and a few other phyla.
Patescibacteria
The superphylum Patescibacteria was originally proposed to encompass the phyla
Sphingobacteria
The
Microgenomates
Microgenomates was originally thought to be a single phylum although evidence suggests it actually encompasses over 11 bacterial phyla,[18][4] including Curtisbacteria, Daviesbacteria, Levybacteria, Gottesmanbacteria, Woesebacteria, Amesbacteria, Shapirobacteria, Roizmanbacteria, Beckwithbacteria, Collierbacteria, Pacebacteria.
Parcubacteria
Parcubacteria was originally described as a single phylum using fewer than 100 16S rRNA sequences. With a greater diversity of 16S rRNA sequences from uncultured organisms now available, it is estimated it may consist of up to 28 bacterial phyla.[2] In line with this, over 14 phyla have now been described within the Parcubacteria group,[18][4] including Kaiserbacteria, Adlerbacteria, Campbellbacteria, Nomurabacteria, Giovannonibacteria, Wolfebacteria, Jorgensenbacteria, Yanofskybacteria, Azambacteria, Moranbacteria, Uhrbacteria, and Magasanikbacteria.
Proteobacteria
It has been proposed that some classes of the phylum
Planctobacteria
The
Terrabacteria
The proposed superphylum, Terrabacteria,[72] includes Actinomycetota, "Cyanobacteria"/"Melainabacteria"-group, Deinococcota, Chloroflexota, Bacillota, and candidate phylum OP10.[72][73][26][69]
Cryptic superphyla
Several candidate phyla (
Historical perspective
Given the rich history of the field of bacterial taxonomy and the rapidity of changes therein in modern times, it is often useful to have a historical perspective on how the field has progressed in order to understand references to antiquated definitions or concepts.
When bacterial nomenclature was controlled under the
In 1987, Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, listed below.[75][76]
- Purple Bacteria and their relatives (later renamed Proteobacteria[77])
- Rickettsiae, Nitrobacter)
- beta subdivision (Rhodocyclus, (some) Thiobacillus, Alcaligenes, Spirillum, Nitrosovibrio)
- gamma subdivision (enterics, fluorescent pseudomonads, purple sulfur bacteria, Legionella, (some) Beggiatoa)
- )
- Gram-positive Eubacteria[Note 1]
- High-G+C species (later renamed Actinobacteria[81]) (Actinomyces, Streptomyces, Arthrobacter, Micrococcus, Bifidobacterium)
- )
- Photosynthetic species (Heliobacteria)
- Species with Gram-negative walls (Megasphaera, Sporomusa)
- Cyanobacteria and chloroplasts (Aphanocapsa, Oscillatoria, Nostoc, Synechococcus, Gloeobacter, Prochloron)
- Spirochetesand relatives
- Spirochetes (Spirochaeta, Treponema, Borrelia)
- Leptospiras (Leptospira, Leptonema)
- Green sulfur bacteria (Chlorobium, Chloroherpeton)
- Flavobacteria and relatives (later renamed Bacteroidetes
- Bacteroides (Bacteroides, Fusobacterium)
- Flavobacterium group (Flavobacterium, Cytophaga, Saprospira, Flexibacter)
- Planctomycetes)
- Planctomyces group (Planctomyces, Pasteuria [sic][Note 2])
- Thermophiles (Isocystis pallida)
- Chlamydiae (Chlamydia psittaci, Chlamydia trachomatis)
- Radioresistant micrococci and relatives (later renamed
- Deinococcus group (Deinococcus radiodurans)
- Thermophiles (Thermus aquaticus)
- Green non-sulfur bacteria and relatives (later renamed Chloroflexi[86])
- Chloroflexus group (Chloroflexus, Herpetosiphon)
- Thermomicrobium group (Thermomicrobium roseum)
- Chloroflexus group (
- Thermotogae (Thermotoga maritima)
Traditionally,
The advent of molecular sequencing technologies has allowed for the recovery of genomes directly from environmental samples (i.e. bypassing culturing), leading to rapid expansion of our knowledge of the diversity of bacterial phyla. These techniques are genome-resolved
See also
- Bacterial taxonomy#Phyla endings
- International Code of Nomenclature of Bacteria
- Branching order of bacterial phyla (Woese, 1987)
- Branching order of bacterial phyla (Gupta, 2001)
- Branching order of bacterial phyla (Cavalier-Smith, 2002)
- Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
- Branching order of bacterial phyla (Battistuzzi et al.,2004)
- Branching order of bacterial phyla (Ciccarelli et al., 2006)
- Branching order of bacterial phyla after ARB Silva Living Tree
- Branching order of bacterial phyla (Genome Taxonomy Database, 2018)
- List of Bacteria genera
- List of bacterial orders
- List of sequenced bacterial genomes
Footnotes
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