Bacterial phyla

Phylogenetic tree showing the diversity of Bacteria, Archaea, and Eukaryota.[1] Major lineages are assigned arbitrary colours and named, with well-characterized lineage names, in italics. Lineages lacking an isolated representative are highlighted with non-italicized names and red dots.

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.[2] As of May 2020, 41 bacterial phyla are formally accepted by the LPSN,[3] 89 bacterial phyla are recognized on the Silva database, dozens more have been proposed,[4][5] and hundreds likely remain to be discovered.[2] As of 2017, approximately 72% of widely recognized bacterial phyla were candidate phyla[6] (i.e. have no cultured representatives).

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

[edit]

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

[edit]

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)

[edit]
Main article: Candidate phyla radiation

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

[edit]

The superphylum Patescibacteria was originally proposed to encompass the phyla Microgenomates (OP11), Parcubacteria (OD1), and Gracilibacteria (GNO2 / BD1-5).[26] More recent phylogenetic analyses show that the last common ancestor of these taxa is the same node as that of CPR.[68]

Sphingobacteria

[edit]
Main article: Sphingobacteria

The Sphingobacteria (FCB group) includes Bacteroidota, Calditrichota, Chlorobiota, candidate phylum "Cloacimonetes", Fibrobacterota, Gemmatimonadota, Ignavibacteriota, candidate phylum "Latescibacteria", candidate phylum "Marinimicrobia", and candidate phylum "Zixibacteria".[26][69]

Microgenomates

[edit]

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

[edit]

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

[edit]

It has been proposed that some classes of the phylum Proteobacteria may be phyla in their own right, which would make Proteobacteria a superphylum.[70] For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes.[71]

Planctobacteria

[edit]
Main article: Planctobacteria

The Planctobacteria (PVC group) includes Chlamydiota, Lentisphaerota, candidate phylum "Omnitrophica", Planctomycetota, candidate phylum "Poribacteria", and Verrucomicrobiota.[26][69]

Terrabacteria

[edit]
Main article: Terrabacteria

The proposed superphylum, Terrabacteria,[72] includes Actinomycetota, "Cyanobacteria"/"Melainabacteria"-group, Deinococcota, Chloroflexota, Bacillota, and candidate phylum OP10.[72][73][26][69]

Cryptic superphyla

[edit]

Several candidate phyla (Microgenomates, Omnitrophica, Parcubacteria, and Saccharibacteria) and several accepted phyla (Elusimicrobiota, Caldisericota, and Armatimonadota) have been suggested to actually be superphyla that were incorrectly described as phyla because rules for defining a bacterial phylum are lacking or due to a lack of sequence diversity in databases when the phylum was first established.[2] For example, it is suggested that candidate phylum Parcubacteria is actually a superphylum that encompasses 28 subordinate phyla and that phylum Elusimicrobia is actually a superphylum that encompasses 7 subordinate phyla.[70]

Historical perspective

[edit]
For historical classifications of bacteria, see Bacterial taxonomy.
For branching order, see Branching order of bacterial phyla (Woese, 1987).
Atomic structure of the 30S ribosomal Subunit from Thermus thermophilus of which 16S makes up a part. Proteins are shown in blue and the single RNA strand in tan.[74]

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 Botanical Code, the term division was used, but now that bacterial nomenclature (with the exception of cyanobacteria) is controlled under the Bacteriological Code, the term phylum is preferred.

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]

Traditionally, phylogeny was inferred and taxonomy established based on studies of morphology. The advent of molecular phylogenetics has allowed for improved elucidation of the evolutionary relationship of species by analyzing their DNA and protein sequences, for example their ribosomal DNA.[87] The lack of easily accessible morphological features, such as those present in animals and plants, hampered early efforts of classification and resulted in erroneous, distorted and confused classification, an example of which, noted Carl Woese, is Pseudomonas whose etymology ironically matched its taxonomy, namely "false unit".[75] Many bacterial taxa were re-classified or re-defined using molecular phylogenetics.

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 metagenomics and single-cell genomics.

See also

[edit]

Footnotes

[edit]
  1. ^ Until recently, it was believed than only Bacillota and Actinomycetota were Gram-positive. However, the candidate phylum TM7 may also be Gram positive.[78] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions[79]).[80]
  2. ^ Pasteuria is now assigned to phylum Bacillota, not to phylum Planctomycetota.
  3. ^ It has been proposed to call the clade Xenobacteria[83] or Hadobacteria[84] (the latter is considered an illegitimate name[85]).

References

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