Bacterial phyla

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Phylogenetic tree showing the diversity of Bacteria, Archaea, and Eukaryota. 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. A Novel Representation Of The Tree Of Life.png
Phylogenetic tree showing the diversity of Bacteria, Archaea, and Eukaryota. 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]

Contents

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

The following is a list of bacterial phyla that have been validly published (not current).

PhylumAlternative namesGroupCultured representativeNotes
10bav-F6 [9] No
"Abawacabacteria" [4] [10] RIF46CPR; Gracilibacteria-related CPRNo
"Abditibacteriota" [11] FBPYes [11]
"Absconditabacteria" [12] [10] SR1CPR; Gracilibacteria-related CPRNo
ABY1 [13] OD1-ABY1 [14] CPR; ParcubacteriaNo
"Bipolaricaulota" [15] OP1, "Acetothermia"
Acidobacteriota "Acidobacteria"Yes [16]
Actinomycetota "Actinobacteria"TerrabacteriaYes [17]
"Adlerbacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4No
"Aerophobota" / "Aerophobetes"CD12, BHI80-139
"Amesbacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Andersenbacteria" [4] RIF9CPR; Parcubacteria; Parcubacteria 4-relatedNo
Armatimonadota [15] "Armatimonadetes", OP10TerrabacteriaYes [19]
"Aminicenantes" [15] OP8
AncK6 [9]
Apal-E12 [9]
Atribacterota [15] OP9, JS1No
Aquificota "Aquificae"
"Azambacteria" i [18] [10] CPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNosplit by Anantharaman et al. …
"Azambacteria" ii [18] [10] CPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNo… (Oct 2016) as being polyphyletic
Bacteroidota "Bacteroidetes"FCB groupYes
Balneolota [20] Yes
Bdellovibrionota
"Beckwithbacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Berkelbacteria" [21] [10] ACD58CPR; Saccharibacteria-related CPRNo
BHI80-139 [9]
"Blackburnbacteria" [4] RIF35CPR; MicrogenomatesNo
"Brennerbacteria" [4] [10] RIF18CPR; Parcubacteria; Parcubacteria 3No
"Brownbacteria" [22] CPR; Parcubacteria; unclassified ParcubacteriaNo
"Buchananbacteria" [4] [10] RIF37CPR; Parcubacteria; Parcubacteria 1No
Caldisericota [15] OP5, [23] "Caldiserica"FCB groupYes [24]
Calditrichota [25] FCB group [26]
"Calescamantes"EM19
"Campbellbacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4Noseem to be polyphyletic: two clades
Campylobacterota
Chlamydiota "Chlamydiae" [27] PVC group
Chlorobiota "Chlorobi"FCB group
Chloroflexota "Chloroflexi""Terrabacteria"
Chisholmbacteria [4] RIF36CPR; "Microgenomates"No
Chrysiogenota "Chrysiogenetes"
"Cloacimonetes" [28] WWE1FCB group [26]
"Coatesbacteria" [4] RIF8No
"Collierbacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Colwellbacteria" [4] [10] RIF41CPR; Parcubacteria; Parcubacteria 3No
Coprothermobacterota
"Curtissbacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
CPR-1 [1] CPRNo
CPR-3 [1] CPRNo
"Cyanobacteria"Terrabacteria
"Dadabacteria" [29] No
"Daviesbacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Delphibacteria" [6] FCB groupNo
"Delongbacteria" [4] RIF26, H-178No
Deferribacterota Deferribacteres
Deinococcota Deinococcus–ThermusTerrabacteria
"Dependentiae" [30] TM6
Dictyoglomota Dictyoglomi [31]
"Dojkabacteria" [10] WS6CPR; Microgenomates-related CPR
"Dormibacteraeota" [32] AD3No
"Doudnabacteria" [18] [10] SM2F11CPR; Parcubacteria; Parcubacteria 1-relatedNo
"Edwardsbacteria" [5] [4] RIF29, UBP-2 [33] No
"Eisenbacteria" [4] RIF28FCB groupNo
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 1No
"Fermentibacteria" [37] Hyd24-12No
"Fertabacteria" [6] CPR; Gracilibacteria-related CPRNo
Fibrobacterota "Fibrobacteres"FCB group
"Firestonebacteria" [4] RIF1No
"Fervidibacteria"OctSpa1-106
"Fischerbacteria" [4] RIF25No
Bacillota "Firmicutes"Terrabacteria
"Fraserbacteria" [4] RIF31No
Fusobacteriota "Fusobacteria"
Gemmatimonadota Gemmatimonadetes [38] FCB group [26] Yes [38]
"Glassbacteria" [4] RIF5No
"Giovannonibacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4-relatedNo
"Gottesmanbacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Gracilibacteria" [39] [10] GN02, BD1-5, SN-2CPR; Patescibacteria; Gracilibacteria-related CPRNo
"Gribaldobacteria" [4] [10] CPR; Parcubacteria; Parcubacteria 2No
"Handelsmanbacteria" [4] RIF27No
"Harrisonbacteria" [4] [10] RIF43CPR; Parcubacteria; Parcubacteria 3No
"Howlettbacteria" [10] CPR; Saccharibacteria-related CPRNo
"Hugbacteria" [22] CPR; Parcubacteria; unclassified ParcubacteriaNo
"Hydrogenedentes"NKB19No
Ignavibacteriota "Ignavibacteria", ZB1FCB group
"Jacksonbacteria" [4] [10] RIF38CPR; Parcubacteria; Parcubacteria 1No
"Jorgensenbacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 3No
"Kaiserbacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 4No
"Katanobacteria" [40] [10] WWE3CPR; Microgenomates-relatedNo
"Kazanbacteria" [10] [4] KazanCPR; Saccharibacteria-related CPRNo
"Kerfeldbacteria" [4] [10] RIF4CPR; Parcubacteria; Parcubacteria 1No
Kiritimatiellota
"Komeilibacteria" [4] [10] RIF6CPR; Parcubacteria; Parcubacteria 1Nosometimes misspelled as "Komelilbacteria" [4]
"Kryptonia" [41] No
KSB1No
"Krumholzibacteriota" [33]
"Kuenenbacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1No
"Lambdaproteobacteria" [4] RIF24ProteobacteriaNo
"Latescibacteria"WS3FCB group [26] No
LCP-89 [42]
Lentisphaerota "Lentisphaerae", vadinBE97PVC group
"Levybacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Lindowbacteria" [4] RIF2CPR; Saccharibacteria-related CPRNo
"Liptonbacteria" [4] [10] RIF42CPR; Parcubacteria; Parcubacteria 3No
"Lloydbacteria" [4] [10] RIF45CPR; Parcubacteria; Parcubacteria 4No
"Magasanikbacteria" [18] [43] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1No
"Margulisbacteria" [4] RIF30No
"Marinimicrobia"SAR406, Marine Group AFCB group [26] Yes
"Melainabacteria" [44] No
"Microgenomates" [45] OP11CPR; PatescibacteriaNoSuperphylum
"Modulibacteria" [39] [46] KSB3, GN06No
"Moranbacteria" [18] [10] OD1-i [18] CPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNo
"Muproteobacteria" [4] RIF23ProteobacteriaNo
Myxococcota
NC10 [47] [13] No
"Nealsonbacteria" [4] [10] RIF40CPR; Parcubacteria; Parcubacteria 2No
"Niyogibacteria" [4] RIF11CPR; Parcubacteria; Parcubacteria 4-relatedNo
Nitrospinota "Nitrospinae" [48] Yes [49] [50]
Nitrospirota "Nitrospirae"Yes
"Nomurabacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 1No
"Omnitrophica" [15] OP3PVC groupNo
"Pacebacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Parcubacteria" [12] OD1CPRNoSuperphylum
"Parcubacteria" 1 [10] CPR; ParcubacteriaNo
"Parcubacteria" 2 [10] CPR; ParcubacteriaNo
"Parcubacteria" 3 [10] CPR; ParcubacteriaNo
"Parcubacteria" 4 [10] CPR; ParcubacteriaNo
"Parcunitrobacteria" [51] CPR; Parcubacteria; unclassified Parcubacteria [52] NoSuperphylum
PAUC34f [53] sponge‐associated unclassified lineage (SAUL)FCB group
"Peregrinibacteria" [54] [55] [56] [57] [10] PERCPR; Gracilibacteria-related CPRNo
"Peribacteria" [10] CPR; Gracilibacteria-related CPRNo
Planctomycetota "Planctomycetes"PVC group
"Poribacteria" [58] PVC group
"Portnoybacteria" [4] RIF22CPR; Parcubacteria; Parcubacteria 4-relatedNo
Pseudomonadota "Proteobacteria"
"Raymondbacteria" [4] RIF7No
Riflebacteria [4] RIF32No
Rhodothermota
"Roizmanbacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Rokubacteria" [29] No
"Ryanbacteria" [4] [10] RIF10CPR; Parcubacteria; Parcubacteri 4-relatedNo
"Saccharibacteria" [30] [10] TM7CPR; Saccharibacteria-related CPRYes
"Saltatorellota" [59]
"Schekmanbacteria" [4] RIF3ProteobacteriaNo
"Shapirobacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Spechtbacteria" [4] [10] RIF19CPR; Parcubacteria; Parcubacteria 2No
Spirochaetota "Spirochaetes"
"Staskawiczbacteria" [4] [10] RIF20CPR; Parcubacteria; Parcubacteria 2No
"Sumerlaeota" [60] [61] BRC1
"Sungbacteria" [4] [10] RIF17CPR; Parcubacteria; Parcubacteria 4-relatedNo
Synergistota "Synergistetes"
TA06 [62] No
"Tagabacteria" [4] [10] RIF12CPR; Parcubacteria; Parcubacteria 4-relatedNo
"Taylorbacteria" [4] [10] RIF16CPR; Parcubacteria; Parcubacteria 4No
"Tectomicrobia" [63]
Mycoplasmatota "Tenericutes"
"Terrybacteria" [4] [10] RIF13CPR; Parcubacteria; Parcubacteria 2No
Thermodesulfobacteriota "Thermodesulfobacteria"
Thermomicrobiota "Thermomicrobia"
Thermotogota "Thermotogae", OP2, EM3 [23] Yes [64]
"Torokbacteria" [10] CPR; Parcubacteria; unclssified ParcubacteriaNo
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 1Noseem to be polyphyletic: two clades
"Veblenbacteria" [4] RIF39CPR; Parcubacteria; Parcubacteria 1-relatedNo
Verrucomicrobiota "Verrucomicrobia"PVC group
"Vogelbacteria" [4] [10] RIF14CPR; Parcubacteria; Parcubacteria 4No
"Wallbacteria" [4] RIF33No
"Wildermuthbacteria" [4] [10] RIF21CPR; Parcubacteria; Parcubacteria 2No
"Wirthbacteria" [65] CPR-related bacteriaNo
"Woesebacteria" [18] CPR; Patescibacteria; MicrogenomatesNo
"Wolfebacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; Parcubacteria 3No
"Woykebacteria" [4] [22] RIF34CPR; MicrogenomatesNo
WOR-1 [62] No
WOR-2 [62] No
WOR-3 [62] No
"Yanofskybacteria" [18] [10] CPR; Patescibacteria; Parcubacteria; unclassified ParcubacteriaNo
"Yonathbacteria" [4] [10] RIF44CPR; Parcubacteria; Parcubacteria 4No
"Zambryskibacteria" [4] [10] RIF15CPR; Parcubacteria; Parcubacteria 4No
ZB2OD1-ZB2 [14] CPR; ParcubacteriaNo
"Zixibacteria" [66] FCB groupNo

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 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

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

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 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

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

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 (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

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. 010 small subunit-1FKA.gif
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.

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

Footnotes

  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] ).

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<span class="mw-page-title-main">Pseudomonadota</span> Phylum of Gram-negative bacteria

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<span class="mw-page-title-main">Acidobacteriota</span> Phylum of bacteria

Acidobacteriota is a phylum of Gram-negative bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.

<span class="mw-page-title-main">Chlamydiota</span> Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

Fibrobacterota is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter was removed from the genus Bacteroides in 1988.

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<span class="mw-page-title-main">Gammaproteobacteria</span> Class of bacteria

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<span class="mw-page-title-main">Terrabacteria</span> Taxon of land bacteria

Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla as well as the phyla "Cyanobacteria", Chloroflexota, and Deinococcota.

<span class="mw-page-title-main">Saccharibacteria</span> Bacterial lineage

Saccharibacteria, formerly known as TM7, is a major bacterial lineage. It was discovered through 16S rRNA sequencing.

<span class="mw-page-title-main">Zetaproteobacteria</span> Class of bacteria

The class Zetaproteobacteria is the sixth and most recently described class of the Pseudomonadota. Zetaproteobacteria can also refer to the group of organisms assigned to this class. The Zetaproteobacteria were originally represented by a single described species, Mariprofundus ferrooxydans, which is an iron-oxidizing neutrophilic chemolithoautotroph originally isolated from Kamaʻehuakanaloa Seamount in 1996 (post-eruption). Molecular cloning techniques focusing on the small subunit ribosomal RNA gene have also been used to identify a more diverse majority of the Zetaproteobacteria that have as yet been unculturable.

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Zixibacteria is a bacterial phylum with candidate status, meaning it had no cultured representatives. It is a member of the FCB group

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<span class="mw-page-title-main">NC10 phylum</span> Phylum of bacteria

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Ann Patricia Wood is a retired British biochemist and bacteriologist who specialized in the ecology, taxonomy and physiology of sulfur-oxidizing chemolithoautotrophic bacteria and how methylotrophic bacteria play a role in the degradation of odour causing compounds in the human mouth, vagina and skin. The bacterial genus Annwoodia was named to honor her contributions to microbial research in 2017.

References

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