Bacterial phyla

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]

Phylogenetic tree showing the diversity of Bacteria, Archaea, and Eukaryota.[1] The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic supergroups. 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.

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).

There are no fixed rules to the nomenclature of bacterial phyla. It was proposed that the suffix "-bacteria" be used for phyla.

List of bacterial phyla

The following is a list of bacterial phyla that have been proposed.

Phylum Alternative names Group Cultured representative Notes
10bav-F6[7] No
Abawacabacteria[4][8] RIF46 CPR; Gracilibacteria-related CPR No
Abditibacteriota[9] FBP Yes[9]
Absconditabacteria[10][8] SR1 CPR; Gracilibacteria-related CPR No
ABY1[11] OD1-ABY1[12] CPR; Parcubacteria No
Acetothermia[13] OP1
Acidobacteria Yes[14]
Actinobacteria Terrabacteria Yes[15]
Adlerbacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4 No
Aerophobota / Aerophobetes CD12, BHI80-139
Amesbacteria[16] CPR; Patescibacteria;

Microgenomates

 No
Andersenbacteria[4] RIF9 CPR; Parcubacteria; Parcubacteria 4-related No
Armatimonadetes[13] OP10 Terrabacteria Yes[17]
Aminicenantes[13] OP8
AncK6[7]
Apal-E12[7]
Atribacteria[13] OP9, JS1 No
Aquificae
Azambacteria i[16][8] CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria No splitted by Anantharaman et al. …
Azambacteria ii[16][8] CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria No … (Oct 2016) as being polyphyletic
Bacteroidetes FCB group Yes
Balneolaeota[18] Yes
Bdellovibrionota
Beckwithbacteria[16] CPR; Patescibacteria; Microgenomates No
Berkelbacteria[19][8] ACD58 CPR; Saccharibacteria-related CPR No
BHI80-139[7]
Blackburnbacteria[4] RIF35 CPR; Microgenomates No
Brennerbacteria[4][8] RIF18 CPR; Parcubacteria; Parcubacteria 3 No
Brownbacteria[20] CPR; Parcubacteria; unclassified Parcubacteria No
Buchananbacteria[4][8] RIF37; Parcubacteria; Parcubacteria 1 CPR No
Caldiserica[13] OP5[21] FCB group Yes[22]
Calditrichaeota[23] Caldithrix FCB group[24]
Calescamantes EM19
Campbellbacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4 No seem to be polyphyletic: two clades
Chlamydiae[25] PVC group
Chlorobi FCB group
Chloroflexi Terrabacteria
Chisholmbacteria[4] RIF36 CPR; Microgenomates No
Chrysiogenetes
Cloacimonetes[26] WWE1 FCB group[24]
Coatesbacteria[4] RIF8 No
Collierbacteria[16] CPR; Patescibacteria; Microgenomates No
Colwellbacteria[4][8] RIF41 CPR; Parcubacteria; Parcubacteria 3 No
Curtissbacteria[16] CPR; Patescibacteria; Microgenomates No
CPR-1[1] CPR No
CPR-3[1] CPR No
Cyanobacteria Terrabacteria
Dadabacteria[27] No
Daviesbacteria[16] CPR; Patescibacteria; Microgenomates No
Delphibacteria[6] FCB group No
Delongbacteria[4] RIF26, H-178 No
Deferribacteres
Deinococcus–Thermus Terrabacteria
Dependentiae[28] TM6
Dictyoglomi[29]
Dojkabacteria[8] WS6 CPR; Microgenomates-related CPR
Dormibacteraeota[30] AD3 No
Doudnabacteria[16][8] SM2F11 CPR; Parcubacteria; Parcubacteria 1-related No
Edwardsbacteria[5][4] RIF29, UBP-2 [31] No
Eisenbacteria[4] RIF28 FCB group No
Elusimicrobia[13] OP7, Termite Group 1 (TG1)[21] Yes[32]
Eremiobacteraeota[33][30] WPS-2, Palusbacterota[34] No
Falkowbacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 No
Fermentibacteria[35] Hyd24-12 No
Fertabacteria[6] CPR; Gracilibacteria-related CPR No
Fibrobacteres FCB group
Firestonebacteria[4] RIF1 No
Fervidibacteria OctSpa1-106
Fischerbacteria[4] RIF25 No
Firmicutes Terrabacteria
Fraserbacteria[4] RIF31 No
Fusobacteria
Gemmatimonadetes[36] FCB group[24] Yes[36]
Glassbacteria[4] RIF5 No
Giovannonibacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4-related No
Gottesmanbacteria[16] CPR; Patescibacteria; Microgenomates No
Gracilibacteria[37][8] GN02, BD1-5, SN-2 CPR; Patescibacteria; Gracilibacteria-related CPR No
Gribaldobacteria[4][8] CPR; Parcubacteria; Parcubacteria 2 No
Handelsmanbacteria[4] RIF27 No
Harrisonbacteria[4][8] RIF43 CPR; Parcubacteria; Parcubacteria 3 No
Howlettbacteria[8] CPR; Saccharibacteria-related CPR No
Hugbacteria[20] CPR; Parcubacteria; unclassified Parcubacteria No
Hydrogenedentes NKB19 No
Ignavibacteria ZB1 FCB group
Jacksonbacteria[4][8] RIF38 CPR; Parcubacteria; Parcubacteria 1 No
Jorgensenbacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 3 No
Kaiserbacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4 No
Katanobacteria[38][8] WWE3 CPR; Microgenomates-related No
Kazanbacteria[8][4] CPR; Saccharibacteria-related CPR No
Kerfeldbacteria[4][8] RIF4 CPR; Parcubacteria; Parcubacteria 1 No
Komeilibacteria[4][8] RIF6 CPR; Parcubacteria; Parcubacteria 1 No sometimes misspelled as "Komelilbacteria"[4]
Kryptonia[39] No
KSB1 No
Krumholzibacteriota[31]
Kuenenbacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 No
Lambdaproteobacteria[4] RIF24 Proteobacteria No
Latescibacteria WS3 FCB group[24] No
LCP-89[40]
Lentisphaerae vadinBE97 PVC group
Levybacteria[16] CPR; Patescibacteria; Microgenomates No
Lindowbacteria[4] RIF2 CPR; Saccharibacteria-related CPR No
Liptonbacteria[4][8] RIF42 CPR; Parcubacteria; Parcubacteria 3 No
Lloydbacteria[4][8] RIF45 CPR; Parcubacteria; Parcubacteria 4 No
Magasanikbacteria[16][41][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 No
Margulisbacteria[4] RIF30 No
Marinimicrobia SAR406, Marine Group A FCB group[24] Yes
Melainabacteria[42] No
Microgenomates[43] OP11 CPR; Patescibacteria No Superphylum
Modulibacteria[37][44] KSB3, GN06 No
Moranbacteria[16][8] OD1-i[16] CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria No
Muproteobacteria[4] RIF23 Proteobacteria No
NC10[45][11] No
Nealsonbacteria[4][8] RIF40 CPR; Parcubacteria; Parcubacteria 2 No
Niyogibacteria[4] RIF11 CPR; Parcubacteria; Parcubacteria 4-related No
Nitrospinae[46]
Nitrospirae
Nomurabacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 No
Omnitrophica[13] OP3 PVC group No
Pacebacteria[16] CPR; Patescibacteria; Microgenomates No
Parcubacteria[10] OD1 CPR No Superphylum
Parcubacteria 1[8] CPR; Parcubacteria No
Parcubacteria 2[8] CPR; Parcubacteria No
Parcubacteria 3[8] CPR; Parcubacteria No
Parcubacteria 4[8] CPR; Parcubacteria No
Parcunitrobacteria[47] CPR; Parcubacteria; unclassified Parcubacteria[48] No Superphylum
PAUC34f[49] sponge‐associated unclassified lineage (SAUL) FCB group
Peregrinibacteria[50][51][52][53][8] PER CPR; Gracilibacteria-related CPR No
Peribacteria[8] CPR; Gracilibacteria-related CPR No
Planctomycetes PVC group
Poribacteria[54] PVC group
Portnoybacteria[4] RIF22 CPR; Parcubacteria; Parcubacteria 4-related No
Proteobacteria
Raymondbacteria[4] RIF7 No
Riflebacteria[4] RIF32 No
Roizmanbacteria[16] CPR; Patescibacteria; Microgenomates No
Rokubacteria[27] No
Ryanbacteria[4][8] RIF10 CPR; Parcubacteria; Parcubacteri 4-related No
Saccharibacteria[28][8] TM7 CPR; Saccharibacteria-related CPR Yes
Saltatorellota[55]
Schekmanbacteria[4] RIF3 Proteobacteria No
Shapirobacteria[16] CPR; Patescibacteria; Microgenomates No
Spechtbacteria[4][8] RIF19 CPR; Parcubacteria; Parcubacteria 2 No
Spirochaetes
Staskawiczbacteria[4][8] RIF20 CPR; Parcubacteria; Parcubacteria 2 No
Sumerlaeota[56][57] BRC1
Sungbacteria[4][8] RIF17 CPR; Parcubacteria; Parcubacteria 4-related No
Synergistetes
TA06[58] No
Tagabacteria[4][8] RIF12 CPR; Parcubacteria; Parcubacteria 4-related No
Taylorbacteria[4][8] RIF16 CPR; Parcubacteria; Parcubacteria 4 No
Tectomicrobia[59]
Tenericutes
Terrybacteria[4][8] RIF13 CPR; Parcubacteria; Parcubacteria 2 No
Thermodesulfobacteria
Thermomicrobia
Thermotogae OP2, EM3[21] Yes[60]
Torobacteria[8] 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[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1 No seem to be polyphyletic: two clades
Veblenbacteria[4] RIF39 CPR; Parcubacteria; Parcubacteria 1-related No
Verrucomicrobia PVC group
Vogelbacteria[4][8] RIF14 CPR; Parcubacteria; Parcubacteria 4 No
Wallbacteria[4] RIF33 No
Wildermuthbacteria[4][8] RIF21 CPR; Parcubacteria; Parcubacteria 2 No
Wirthbacteria[61] CPR-related bacteria No
Woesebacteria[16] CPR; Patescibacteria; Microgenomates No
Wolfebacteria[16][8] CPR; Patescibacteria; Parcubacteria; Parcubacteria 3 No
Woykebacteria[4][20] RIF34 CPR; Microgenomates No
WOR-1[58] No
WOR-2[58] No
WOR-3[58] No
Yanofskybacteria[16][8] CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria No
Yonathbacteria[4][8] RIF44 CPR; Parcubacteria; Parcubacteria 4 No
Zambryskibacteria[4][8] RIF15 CPR; Parcubacteria; Parcubacteria 4 No
ZB2 OD1-ZB2[12] CPR; Parcubacteria No
Zixibacteria[62] 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)
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.[63] 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 Microgenomates (OP11), Parcubacteria (OD1), and Gracilibacteria (GNO2 / BD1-5).[24] More recent phylogenetic analyses show that the last common ancestor of these taxa is the same node as that of CPR.[64]

Sphingobacteria
Main article: Sphingobacteria

The Sphingobacteria (FCB group) includes Bacteroidetes, Calditrichaeota, Chlorobi, candidate phylum Cloacimonetes, Fibrobacteres, Gemmatimonadates, candidate phylum Ignavibacteriae, candidate phylum Latescibacteria, candidate phylum Marinimicrobia, and candidate phylum Zixibacteria.[24][65]

Microgenomates

Microgenomates was originally thought to be a single phylum although evidence suggests it actually encompasses over 11 bacterial phyla,[16][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,[16][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 Proteobacteria may be phyla in their own right, which would make Proteobacteria a superphylum.[66] For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes.[67]

Planctobacteria
Main article: Planctobacteria

The Planctobacteria (PVC group) includes Chlamydiae, Lentisphaerae, candidate phylum Omnitrophica, Planctomycetes, candidate phylum Poribacteria, and Verrucomicrobia.[24][65]

Terrabacteria

The proposed superphylum, Terrabacteria,[68] includes Actinobacteria, Cyanobacteria, Deinococcus–Thermus, Chloroflexi, Firmicutes, and candidate phylum OP10.[68][69][24][65]

Cryptic superphyla

Several candidate phyla (Microgenomates, Omnitrophica, Parcubacteria, and Saccharibacteria) and several accepted phyla (Elusimicrobia, Caldiserica, and Armatimonadetes) 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 establish.[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.[66]

Historical perspective
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.[70]

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.[71][72]

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.[83] 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".[71] 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

Footnotes
  1. Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. However, the candidate phylum TM7 may also be Gram positive.[74] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions[75]).[76]
  2. Pasteuria is now assigned to phylum Bacilli, not to phylum Planctomycetes.
  3. It has been proposed to call the clade Xenobacteria[79] or Hadobacteria[80] (the latter is considered an illegitimate name[81]).

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