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.
It has been estimated that ~1,300 bacterial phyla exist. As of May 2020, 41 bacterial phyla are formally accepted by the LPSN, 89 bacterial phyla are recognized on the , dozens more have been proposed, and hundreds likely remain to be discovered. As of 2017, approximately 72% of widely recognized bacterial phyla were candidate phyla.
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.
PhylumAlternative namesGroupCultured representativeNotes
10bav-F6No
AbawacabacteriaRIF46CPRNo
AbditibacteriotaFBPYes
AbsconditabacteriaSR1CPRNo
AcetothermiaOP1
AcidobacteriaYes
ActinobacteriaYes
AdlerbacteriaCPR; Patescibacteria; ParcubacteriaNo
Aerophobota / AerophobetesCD12, BHI80-139
AmesbacteriaCPR; Patescibacteria;
Microgenomates		No
AndersenbacteriaRIF9CPRNo
ArmatimonadetesOP10Yes
AminicenantesOP8
AncK6
Apal-E12
AtribacteriaOP9, JS1No
Aquificae
AzambacteriaCPR; Patescibacteria; ParcubacteriaNo
BacteroidetesFCB groupYes
BalneolaeotaYes
Bdellovibrionota
BeckwithbacteriaCPR; Patescibacteria; MicrogenomatesNo
BHI80-139
BerkelbacteriaACD58CPRNo
BlackburnbacteriaRIF35CPRNo
BrennerbacteriaRIF18CPRNo
BuchananbacteriaRIF37CPRNo
CaldisericaOP5Yes
CalditrichaeotaCaldithrixFCB group
CalescamantesEM19, OP1
CampbellbacteriaCPR; Patescibacteria; ParcubacteriaNo
Chlamydiae
ChlorobiFCB group
Chloroflexi
ChisholmbacteriaRIF36CPRNo
Chrysiogenetes
CloacimonetesWWE1FCB group
CoatesbacteriaRIF8No
CollierbacteriaCPR; Patescibacteria; MicrogenomatesNo
ColwellbacteriaRIF41CPRNo
CurtisbacteriaCPR; Patescibacteria; MicrogenomatesNo
CPR-1
CPR-2CPRNo
Cyanobacteria
DadabacteriaNo
DaviesbacteriaCPR; Patescibacteria; MicrogenomatesNo
DelphibacteriaFCB groupNo
DelongbacteriaRIF26, H-178No
Deferribacteres
Deinococcus–Thermus
DependentiaeTM6
Dictyoglomi
DojkabacteriaWS6
DormibacteraeotaAD3No
DoudnabacteriaSM2F11CPRNo
EdwardsbacteriaRIF29, UBP-2No
EisenbacteriaRIF28FCB groupNo
ElusimicrobiaOP7, Termite Group 1 Yes
EremiobacteraeotaWPS-2, PalusbacterotaNo
FalkowbacteriaCPR; Patescibacteria; ParcubacteriaNo
FermentibacteriaHyd24-12No
FertabacteriaNo
FibrobacteresFCB group
FirestonebacteriaRIF1No
FervidibacteriaOctSpa1-106
FischerbacteriaRIF25No
Firmicutes
FraserbacteriaRIF31No
Fusobacteria
GemmatimonadetesFCB groupYes
GlassbacteriaRIF5No
GiovannonibacteriaCPR; Patescibacteria; ParcubacteriaNo
GottesmanbacteriaCPR; Patescibacteria; MicrogenomatesNo
GracilibacteriaGN02, BD1-5, SN-2CPR; PatescibacteriaNo
HandelsmanbacteriaRIF27No
HarrisonbacteriaRIF43CPRNo
HydrogenedentesNKB19No
IgnavibacteriaZB1
JacksonbacteriaRIF38CPRNo
JorgensenbacteriaCPR; Patescibacteria; ParcubacteriaNo
KaiserbacteriaCPR; Patescibacteria; ParcubacteriaNo
KatanobacteriaWWE3No
KazanCPRNo
KerfeldbacteriaRIF4CPRNo
KomeilibacteriaRIF6CPRNo
KryptoniaNo
KSB1No
Krumholzibacteriota
KuenenbacteriaCPR; Patescibacteria; ParcubacteriaNo
LambdaproteobacteriaRIF24No
LatescibacteriaWS3FCB groupNo
LCP-89
LentisphaeraevadinBE97
LevybacteriaCPR; Patescibacteria; MicrogenomatesNo
LindowbacteriaRIF2No
LiptonbacteriaRIF42CPRNo
LloydbacteriaRIF45CPRNo
MagasanikbacteriaCPR; Patescibacteria; ParcubacteriaNo
MargulisbacteriaRIF30No
MarinimicrobiaSAR406, Marine Group AFCB groupYes
MelainabacteriaNo
MicrogenomatesOP11CPR; PatescibacteriaNoSuperphylum
ModulibacteriaKSB3, GN06No
MoranbacteriaCPR; Patescibacteria; ParcubacteriaNo
MuproteobacteriaRIF23No
NC10No
NealsonbacteriaRIF40CPRNo
NiyogibacteriaRIF11CPRNo
Nitrospinae
Nitrospirae
NomurabacteriaCPR; Patescibacteria; ParcubacteriaNo
OmnitrophicaOP3No
PacebacteriaCPR; Patescibacteria; MicrogenomatesNo
ParcubacteriaOD1CPRNoSuperphylum
PAUC34fsponge‐associated unclassified lineage FCB group
PerigrinibacteriaPERNo
Planctomycetes
Poribacteria
PortnoybacteriaRIF22CPRNo
Proteobacteria
RaymondbacteriaRIF7No
RiflebacteriaRIF32No
RoizmanbacteriaCPR; Patescibacteria; MicrogenomatesNo
RokubacteriaNo
RyanbacteriaRIF10CPRNo
SaccharibacteriaTM7Yes
Saltatorellota
SchekmanbacteriaRIF3CPRNo
ShapirobacteriaCPR; Patescibacteria; MicrogenomatesNo
SpechtbacteriaRIF19CPRNo
Spirochaetes
StaskawiczbacteriaRIF20CPRNo
SumerlaeotaBRC1
SungbacteriaRIF17CPRNo
Synergistetes
TA06No
TagabacteriaRIF12CPRNo
TaylorbacteriaRIF16CPRNo
Tectomicrobia
Tenericutes
TerrybacteriaRIF13CPRNo
Thermodesulfobacteria
Thermomicrobia
ThermotogaeOP2, EM3Yes
UBP-1No
UBP-3No
UBP-4No
UBP-5No
UBP-6No
UBP-7No
UBP-8No
UBP-9No
UBP-10No
UBP-11No
UBP-12No
UBP-13No
UBP-14No
UBP-15No
UBP-16No
UBP-17No
UhrbacteriaCPR; Patescibacteria; ParcubacteriaNo
VeblenbacteriaRIF39CPRNo
Verrucomicrobia
VogelbacteriaRIF14CPRNo
WallbacteriaRIF33No
WildermuthbacteriaRIF21CPRNo
WoesebacteriaCPR; Patescibacteria; MicrogenomatesNo
WolfebacteriaCPR; Patescibacteria; ParcubacteriaNo
WoykebacteriaRIF34CPRNo
WOR-1No
WOR-2No
WOR-3No
YanofskybacteriaCPR; Patescibacteria; ParcubacteriaNo
YonathbacteriaRIF44CPRNo
ZambryskibacteriaRIF15CPRNo
ZixibacteriaNo

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. It includes the Patescibacteria group as well as dozens of additional phyla and superphyla.

Sphingobacteria

The Sphingobacteria includes Bacteroidetes, Calditrichaeota, Chlorobi, candidate phylum Cloacimonetes, Fibrobacteres, Gemmatimonadates, candidate phylum Ignavibacteriae, candidate phylum Latescibacteria, candidate phylum Marinimicrobia, and candidate phylum Zixibacteria.

Microgenomates

Microgenomates was originally thought to be a single phylum although evidence suggests it actually encompasses over 11 bacterial phyla, 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 the diversity of 16S rRNA sequences from uncultured organisms now available, it is estimated it may consist of up to 28 bacterial phyla. In line with this, over 14 phyla have now been described within the Parcubacteria group, including Kaiserbacteria, Adlerbacteria, Campbellbacteria, Nomurabacteria, Giovannonibacteria, Wolfebacteria, Jorgensenbacteria, Yanofskybacteria, Azambacteria, Moranbacteria, Uhrbacteria, and Magasankibacteria,

The superphylum Patescibacteria was originally proposed to encompass the phyla Microgenomates, Parcubacteria, and Gracilibacteria. Unfortunately, the meaning of the term 'Patescibacteria' has become confused and is sometimes erroneously used interchangeably with the term Candidate Phyla Radiation. To complicate matters, it has been suggested that the Microgenomates and Parcubacteria groups within the Patescibacteria are themselves actually superphyla.

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. For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes.

Planctobacteria

The Planctobacteria includes Chlamydiae, Lentisphaerae, candidate phylum Omnitrophica, Planctomycetes, candidate phylum Poribacteria, and Verrucomicrobia.

Terrabacteria

The proposed superphylum, Terrabacteria, includes Actinobacteria, Cyanobacteria, Deinococcus–Thermus, Chloroflexi, Firmicutes, and candidate phylum OP10.

Cryptic superphyla

Several candidate phyla and several accepted phyla 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. For example, it is suggested that candidate phylum Parcubacteria is actually a superphylum that encompasses 28 subordinate phyla and that phylum Elusimocrobia is actually a superphylum that encompasses 7 subordinate 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 Botanical Code, the term division was used, but now that bacterial nomenclature 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 sequences, listed below.
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. 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". 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, leading to rapid expansion of our knowledge of the diversity of bacterial phyla. These techniques are genome-resolved metagenomics and single-cell genomics.

Footnotes