Bacterial phyla

Short description: Phyla of the domain Bacteria

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,[4] dozens more have been proposed,[5][6] and hundreds likely remain to be discovered.[2] As of 2017, approximately 72% of widely recognized bacterial phyla were candidate phyla[7] (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.[8][9]

## Contents

* 1 List of bacterial phyla
* 2 Supergroups
* 2.1 Candidate phyla radiation (CPR)
* 2.2 Patescibacteria
* 2.3 Sphingobacteria
* 2.4 Microgenomates
* 2.5 Parcubacteria
* 2.6 Proteobacteria
* 2.7 Planctobacteria
* 2.8 Bacillati
* 2.9 Cryptic superphyla
* 3 Historical perspective
* 4 See also
* 5 Footnotes
* 6 References

## List of bacterial phyla

The following is a list of bacterial phyla that have been validly published as of December 2023.

Published Phyla  Phylum  | Alternative names  | Group  | Known classes  | Notes

|
|
|
|

"Abditibacteriota"[10] | FBP  |  | 1  |
Acidobacteriota[11] | "Acidobacteria"  |  | 5  |
Actinomycetota[12] | "Actinobacteria"  | Bacillati  | 6  |
Armatimonadota[13][14] | "Armatimonadetes", OP10  | Bacillati  | 3  |
Atribacterota[13] | OP9, JS1  |  | 1  |
Aquificota | "Aquificae"  |  | 3  |
Bacteroidota | "Bacteroidetes"  | FCB group  | 6  |
Balneolota[15] |  |  | 1  |
Bdellovibrionota |  |  | 3  |
Caldisericota[13][16] | OP5,[17] "Caldiserica"  | FCB group  |  |
Calditrichota[18] |  | FCB group[19] |  |
Campylobacterota |  |  | 2  |
Chlamydiota | "Chlamydiae"[20] | PVC group  | 1  |
Chlorobiota  | "Chlorobi"  | FCB group  | 1  |
Chloroflexota | "Chloroflexi"  | Bacillati  |  |
Chrysiogenota | "Chrysiogenetes"  |  |  |
Coprothermobacterota |  |  |  |
Cyanobacteriota | Cyanobacteria  | Bacillati  | 2  |
Deferribacterota  | Deferribacteres  |  |  |
Deinococcota | Deinococcus–Thermus  | Bacillati  | 1  |
Dictyoglomota  | Dictyoglomi[21] |  |  |
Elusimicrobiota[22] | Elusimicrobia, OP7, Termite Group 1 (TG1)[17] |  |  |
Fibrobacterota | "Fibrobacteres"  | FCB group  |  |
Bacillota | "Firmicutes"  | Bacillati  | 9  |
Fusobacteriota | "Fusobacteria"  |  | 1  |
Gemmatimonadota[23] | Gemmatimonadetes[23] | FCB group[19] |  |
Ignavibacteriota  | "Ignavibacteria", ZB1  | FCB group  |  |
Kiritimatiellota |  |  |  |
Lentisphaerota | "Lentisphaerae", vadinBE97  | PVC group  |  |
"Marinimicrobia"  | SAR406, Marine Group A  | FCB group[19] |  |
Myxococcota  |  |  | 3  |
Nitrospinota[24][25] | "Nitrospinae"[26] |  |  |
Nitrospirota | "Nitrospirae"  |  |  |
Planctomycetota | "Planctomycetes"  | PVC group  |  |
Pseudomonadota | "Proteobacteria"  |  |  |
Rhodothermota |  |  |  |
"Saccharibacteria"[27][28] | TM7  | CPR; Saccharibacteria-related CPR  |  |
Spirochaetota  | "Spirochaetes"  |  |  |
Synergistota | "Synergistetes"  |  |  |
Mycoplasmatota | "Tenericutes"  |  |  |
Thermodesulfobacteriota | "Thermodesulfobacteria"  |  |  |
Thermomicrobiota | "Thermomicrobia"  |  |  |
Thermotogota[29] | "Thermotogae", OP2, EM3[17] |  |  |
Verrucomicrobiota | "Verrucomicrobia"  | PVC group  |  |

The following is a list of candidate phyla that have not been cultured.

Candidate Phyla  Phylum  | Alternative Names  | Group  | Notes

|
|
|

"Absconditabacteria"[30][28] | SR1  | CPR; Gracilibacteria-related CPR  |
ABY1[31] | OD1-ABY1[32] | CPR; Parcubacteria  |
"Aerophobota" / "Aerophobetes"  | CD12, BHI80-139  |  |
"Andersenbacteria"[5] | RIF9  | CPR; Parcubacteria; Parcubacteria 4-related  |
"Aminicenantota"[33] | OP8  |  |
"Berkelbacteria"[34][28] | ACD58  | CPR; Saccharibacteria-related CPR  |
"Bipolaricaulota"[13] | OP1, "Acetothermia"  |  |
"Blackburnbacteria"[5] | RIF35  | CPR; Microgenomates  |
"Brennerbacteria"[5][28] | RIF18  | CPR; Parcubacteria; Parcubacteria 3  |
"Brownbacteria"[35] |  | CPR; Parcubacteria; unclassified Parcubacteria  |
"Buchananbacteria"[5][28] | RIF37  | CPR; Parcubacteria; Parcubacteria 1  |
"Campbellbacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 4  | Seems to be polyphyletic; 2 clades
"Cloacimonetes"[37] | WWE1  | FCB group[19] |
"Coatesbacteria"[5] | RIF8  |  |
"Collierbacteria"[36] |  | CPR; Patescibacteria; Microgenomates  |
"Colwellbacteria"[5][28] | RIF41  | CPR; Parcubacteria; Parcubacteria 3  |
"Curtissbacteria"[36] |  | CPR; Patescibacteria; Microgenomates  |
"Dadabacteria"[38] |  |  | No
"Daviesbacteria"[36] |  | CPR; Patescibacteria; Microgenomates  | No
"Delphibacteria"[7] |  | FCB group  | No
"Delongbacteria"[5] | RIF26, H-178  |  | No
"Dependentiae"[27] | TM6  |  |
"Dojkabacteria"[28] | WS6  | CPR; Microgenomates-related CPR  |
"Dormibacteraeota"[39] | AD3  |  |
"Doudnabacteria"[36][28] | SM2F11  | CPR; Parcubacteria; Parcubacteria 1-related  |
"Edwardsbacteria"[6][5] | RIF29, UBP-2 [40] |  |
"Eisenbacteria"[5] | RIF28  | FCB group  |
"Eremiobacteraeota"[41][39] | WPS-2, Palusbacterota[42] |  |
"Falkowbacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1  |
"Fermentibacteria"[43] | Hyd24-12  |  |
"Fertabacteria"[7] |  | CPR; Gracilibacteria-related CPR  |
"Firestonebacteria"[5] | RIF1  |  |
"Fervidibacteria"  | OctSpa1-106  |  |
"Fischerbacteria"[5] | RIF25  |  |
"Fraserbacteria"[5] | RIF31  |  |
"Glassbacteria"[5] | RIF5  |  | No
"Giovannonibacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 4-related  | No
"Gottesmanbacteria"[36] |  | CPR; Patescibacteria; Microgenomates  | No
"Gracilibacteria"[44][28] | GN02, BD1-5, SN-2  | CPR; Patescibacteria; Gracilibacteria-related CPR  | No
"Gribaldobacteria"[5][28] |  | CPR; Parcubacteria; Parcubacteria 2  | No
"Handelsmanbacteria"[5] | RIF27  |  | No
"Harrisonbacteria"[5][28] | RIF43  | CPR; Parcubacteria; Parcubacteria 3  | No
"Howlettbacteria"[28] |  | CPR; Saccharibacteria-related CPR  | No
"Hugbacteria"[35] |  | CPR; Parcubacteria; unclassified Parcubacteria  |
"Hydrogenedentes"  | NKB19  |  |
"Jacksonbacteria"[5][28] | RIF38  | CPR; Parcubacteria; Parcubacteria 1  |
"Jorgensenbacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 3  |
"Kaiserbacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 4  |
"Katanobacteria"[45][28] | WWE3  | CPR; Microgenomates-related  |
"Kazanbacteria"[28][5] | Kazan  | CPR; Saccharibacteria-related CPR  |
"Kerfeldbacteria"[5][28] | RIF4  | CPR; Parcubacteria; Parcubacteria 1  |
"Komeilibacteria"[5][28] | RIF6  | CPR; Parcubacteria; Parcubacteria 1  |
"Kryptonia"[46] |  |  |
"Krumholzibacteriota"[40] |  |  |
"Kuenenbacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1  |
"Lambdaproteobacteria"[5] | RIF24  | Proteobacteria  |
"Latescibacteria"  | WS3  | FCB group[19] |
"Levybacteria"[36] |  | CPR; Patescibacteria; Microgenomates  | No
"Lindowbacteria"[5] | RIF2  | CPR; Saccharibacteria-related CPR  | No
"Liptonbacteria"[5][28] | RIF42  | CPR; Parcubacteria; Parcubacteria 3  | No
"Lloydbacteria"[5][28] | RIF45  | CPR; Parcubacteria; Parcubacteria 4  | No
"Magasanikbacteria"[36][47][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1  | No
"Margulisbacteria"[5] | RIF30  |  | No
"Melainabacteria"[48] |  |  |
"Microgenomates"[49] | OP11  | CPR; Patescibacteria  |
"Modulibacteria"[44][50] | KSB3, GN06  |  |
"Moranbacteria"[36][28] | OD1-i[36] | CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria  |
"Muproteobacteria"[5] | RIF23  | Proteobacteria  |
NC10[51][31] |  |  |
"Nealsonbacteria"[5][28] | RIF40  | CPR; Parcubacteria; Parcubacteria 2  |
"Niyogibacteria"[5] | RIF11  | CPR; Parcubacteria; Parcubacteria 4-related  |
"Nomurabacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1  |
"Omnitrophica"[13] | OP3  | PVC group  |
"Pacebacteria"[36] |  | CPR; Patescibacteria; Microgenomates  |
"Parcubacteria"[30] | OD1  | CPR  |
"Parcubacteria" 1[28] |  | CPR; Parcubacteria  |
"Parcubacteria" 2[28] |  | CPR; Parcubacteria  |
"Parcubacteria" 3[28] |  | CPR; Parcubacteria  |
"Parcubacteria" 4[28] |  | CPR; Parcubacteria  |
"Parcunitrobacteria"[52] |  | CPR; Parcubacteria; unclassified Parcubacteria[53] |
PAUC34f[54] | sponge‐associated unclassified lineage (SAUL)  | FCB group  |
"Peregrinibacteria"[55][56][57][58][28] | PER  | CPR; Gracilibacteria-related CPR  |
"Peribacteria"[28] |  | CPR; Gracilibacteria-related CPR  |
"Poribacteria"[59] |  | PVC group  |
"Portnoybacteria"[5] | RIF22  | CPR; Parcubacteria; Parcubacteria 4-related  |
"Raymondbacteria"[5] | RIF7  |  |
Riflebacteria[5] | RIF32  |  |
"Roizmanbacteria"[36] |  | CPR; Patescibacteria; Microgenomates  |
"Rokubacteria"[38] |  |  |
"Ryanbacteria"[5][28] | RIF10  | CPR; Parcubacteria; Parcubacteri 4-related  |
"Saltatorellota"[60] |  |  |
"Schekmanbacteria"[5] | RIF3  | Proteobacteria  |
"Shapirobacteria"[36] |  | CPR; Patescibacteria; Microgenomates  |
"Spechtbacteria"[5][28] | RIF19  | CPR; Parcubacteria; Parcubacteria 2  |
"Staskawiczbacteria"[5][28] | RIF20  | CPR; Parcubacteria; Parcubacteria 2  |
"Sumerlaeota"[61][62] | BRC1  |  |
"Sungbacteria"[5][28] | RIF17  | CPR; Parcubacteria; Parcubacteria 4-related  |
TA06[63] |  |  |
"Tagabacteria"[5][28] | RIF12  | CPR; Parcubacteria; Parcubacteria 4-related  |
"Taylorbacteria"[5][28] | RIF16  | CPR; Parcubacteria; Parcubacteria 4  |
"Tectomicrobia"[64] |  |  |
"Terrybacteria"[5][28] | RIF13  | CPR; Parcubacteria; Parcubacteria 2  |
"Torokbacteria"[28] |  | CPR; Parcubacteria; unclssified Parcubacteria  |
UBP-1[6] |  |  |
"Uhrbacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 1  |
"Veblenbacteria"[5] | RIF39  | CPR; Parcubacteria; Parcubacteria 1-related  |
"Vogelbacteria"[5][28] | RIF14  | CPR; Parcubacteria; Parcubacteria 4  |
"Wallbacteria"[5] | RIF33  |  |
"Wildermuthbacteria"[5][28] | RIF21  | CPR; Parcubacteria; Parcubacteria 2  |
"Wirthbacteria"[65] |  | CPR-related bacteria  |
"Woesebacteria"[36] |  | CPR; Patescibacteria; Microgenomates  |
"Wolfebacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; Parcubacteria 3  |
"Woykebacteria"[5][35] | RIF34  | CPR; Microgenomates  |
"Yanofskybacteria"[36][28] |  | CPR; Patescibacteria; Parcubacteria; unclassified Parcubacteria  |
"Yonathbacteria"[5][28] | RIF44  | CPR; Parcubacteria; Parcubacteria 4  |
"Zambryskibacteria"[5][28] | RIF15  | CPR; Parcubacteria; Parcubacteria 4  |
ZB2  | OD1-ZB2[32] | CPR; Parcubacteria  |
"Zixibacteria"[66] |  | FCB group  |

## 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. The LPSN recognizes four kingdoms of bacteria as validly published: Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati.[67]

### Candidate phyla radiation (CPR)

Main article: Biology:Candidate phyla radiation

The CPR is a descriptive term referring to a massive monophyletic radiation of candidate phyla that exists within the Bacterial domain.[68] 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).[19] More recent phylogenetic analyses show that the last common ancestor of these taxa is the same node as that of CPR.[69]

### 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".[19][70]

### Microgenomates

Microgenomates was originally thought to be a single phylum although evidence suggests it actually encompasses over 11 bacterial phyla,[36][5] 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,[36][5] 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.[71] For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes.[72]

### Planctobacteria

The Planctobacteria (PVC group) includes Chlamydiota, Lentisphaerota, candidate phylum "Omnitrophica", Planctomycetota, candidate phylum "Poribacteria", and Verrucomicrobiota.[19][70]

### Bacillati

Main article: Biology:Bacillati

The kingdom Bacillati,[73] includes Actinomycetota, "Cyanobacteria/Melainabacteria clade", Deinococcota, Chloroflexota, Bacillota, and candidate phylum OP10.[73][74][19][70]

### 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.[71]

## Historical perspective

For historical classifications of bacteria, see Biology:Bacterial taxonomy.

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.[75]

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.[76][77]

* Purple Bacteria and their relatives (later renamed Proteobacteria[78])
* alpha subdivision (purple non-sulfur bacteria, rhizobacteria, Agrobacterium, Rickettsiae, Nitrobacter)
* beta subdivision (Rhodocyclus, (some) Thiobacillus, Alcaligenes, Spirillum, Nitrosovibrio)
* gamma subdivision (enterics, fluorescent pseudomonads, purple sulfur bacteria, Legionella, (some) Beggiatoa)
* delta subdivision (Sulfur and sulfate reducers (Desulfovibrio), Myxobacteria, Bdellovibrio)
* Gram-positive Eubacteria[Note 1]
* High-G+C species (later renamed Actinobacteria[82]) (Actinomyces, Streptomyces, Arthrobacter, Micrococcus, Bifidobacterium)
* Low-G+C species (later renamed Firmicutes[82]) (Clostridium, Peptococcus, Bacillus, Mycoplasma)
* Photosynthetic species (Heliobacteria)
* Species with Gram-negative walls (Megasphaera, Sporomusa)
* Cyanobacteria and chloroplasts (Aphanocapsa, Oscillatoria, Nostoc, Synechococcus, Gloeobacter, Prochloron)
* Spirochetes and relatives
* Spirochetes (Spirochaeta, Treponema, Borrelia)
* Leptospiras (Leptospira, Leptonema)
* Green sulfur bacteria (Chlorobium, Chloroherpeton)
* Bacteroides, Flavobacteria and relatives (later renamed Bacteroidetes
* Bacteroides (Bacteroides, Fusobacterium)
* Flavobacterium group (Flavobacterium, Cytophaga, Saprospira, Flexibacter)
* Planctomyces and relatives (later renamed Planctomycetes)
* Planctomyces group (Planctomyces, Pasteuria [sic][Note 2])
* Thermophiles (Isocystis pallida)
* Chlamydiae (Chlamydia psittaci, Chlamydia trachomatis)
* Radioresistant micrococci and relatives (later renamed Deinococcus–Thermus[83] or Thermi)[Note 3]
* Deinococcus group (Deinococcus radiodurans)
* Thermophiles (Thermus aquaticus)
* Green non-sulfur bacteria and relatives (later renamed Chloroflexi[87])
* Chloroflexus group (Chloroflexus, Herpetosiphon)
* Thermomicrobium group (Thermomicrobium roseum)
* Thermotogae (Thermotoga maritima)

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.[88] 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".[76] 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

* Bacterial taxonomy
* 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

1. ↑ Until recently, it was believed than only Bacillota and Actinomycetota were Gram-positive. However, the candidate phylum TM7 may also be Gram positive.[79] Chloroflexi however possess a single bilayer, but stain negative (with some exceptions[80]).[81]
2. ↑ Pasteuria is now assigned to phylum Bacillota, not to phylum Planctomycetota.
3. ↑ It has been proposed to call the clade Xenobacteria[84] or Hadobacteria[85] (the latter is considered an illegitimate name[86]).

## References

1. ↑ Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W. et al. (2016-04-11). "A new view of the tree of life" (in en). Nature Microbiology 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. ISSN 2058-5276. PMID 27572647.
2. ↑ 2.0 2.1 2.2 2.3 2.4 Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar; Glöckner, Frank Oliver; Ludwig, Wolfgang; Schleifer, Karl-Heinz; Whitman, William B.; Euzéby, Jean et al. (September 2014). "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences" (in en). Nature Reviews Microbiology 12 (9): 635–645. doi:10.1038/nrmicro3330. ISSN 1740-1534. PMID 25118885. https://www.nature.com/articles/nrmicro3330.
3. ↑ Bacterial phyla entry in LPSN [Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol (Microbiology Society) 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655. https://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/00207713-47-2-590. Retrieved 2019-02-23. ]
4. ↑ "Silva". https://www.arb-silva.de/.
5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 5.13 5.14 5.15 5.16 5.17 5.18 5.19 5.20 5.21 5.22 5.23 5.24 5.25 5.26 5.27 5.28 5.29 5.30 5.31 5.32 5.33 5.34 5.35 5.36 5.37 5.38 5.39 5.40 5.41 5.42 5.43 5.44 5.45 5.46 5.47 5.48 Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; Sharon, Itai; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Singh, Andrea et al. (2016-10-24). "Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system" (in en). Nature Communications 7 (1). doi:10.1038/ncomms13219. ISSN 2041-1723. PMID 27774985. Bibcode: 2016NatCo...713219A.
6. ↑ 6.0 6.1 6.2 Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria; Chaumeil, Pierre-Alain; Woodcroft, Ben J.; Evans, Paul N.; Hugenholtz, Philip; Tyson, Gene W. (November 2017). "Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life" (in en). Nature Microbiology 2 (11): 1533–1542. doi:10.1038/s41564-017-0012-7. ISSN 2058-5276. PMID 28894102.
7. ↑ 7.0 7.1 7.2 Dudek, Natasha K.; Sun, Christine L.; Burstein, David; Kantor, Rose S.; Aliaga Goltsman, Daniela S.; Bik, Elisabeth M.; Thomas, Brian C.; Banfield, Jillian F. et al. (2017-12-18). "Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome". Current Biology 27 (24): 3752–3762.e6. doi:10.1016/j.cub.2017.10.040. ISSN 1879-0445. PMID 29153320. Bibcode: 2017CBio...27E3752D.
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72. ↑ Hug LA (2016). "A new view of the tree of life". Nature Microbiology Article 16048 (5). doi:10.1038/nmicrobiol.2016.48. PMID 27572647.
73. ↑ 73.0 73.1 "A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land". BMC Evolutionary Biology 4. November 2004. doi:10.1186/1471-2148-4-44. PMID 15535883.
74. ↑ Battistuzzi, F. U.; Hedges, S. B. (6 November 2008). "A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land". Molecular Biology and Evolution 26 (2): 335–343. doi:10.1093/molbev/msn247. PMID 18988685.
75. ↑ Schluenzen F (2000). "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution". Cell 102 (5): 615–23. doi:10.1016/S0092-8674(00)00084-2. PMID 11007480.
76. ↑ 76.0 76.1 Woese, CR (1987). "Bacterial evolution". Microbiological Reviews 51 (2): 221–71. doi:10.1128/MMBR.51.2.221-271.1987. PMID 2439888.
77. ↑ Holland L (22 May 1990). "Carl Woese in forefront of bacterial evolution revolution". The Scientist 3 (10). http://www.the-scientist.com/?articles.view/articleNo/11130/title/Carl-Woese-In-Forefront-Of-Bacterial-Evolution-Revolution/.
78. ↑ Stackebrandt (1988). "Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives"". Int. J. Syst. Bacteriol. 38 (3): 321–325. doi:10.1099/00207713-38-3-321.
79. ↑ Hugenholtz, P.; Tyson, G. W.; Webb, R. I.; Wagner, A. M.; Blackall, L. L. (2001). "Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives". Applied and Environmental Microbiology 67 (1): 411–9. doi:10.1128/AEM.67.1.411-419.2001. PMID 11133473. Bibcode: 2001ApEnM..67..411H.
80. ↑ Yabe, S.; Aiba, Y.; Sakai, Y.; Hazaka, M.; Yokota, A. (2010). "Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria". International Journal of Systematic and Evolutionary Microbiology 61 (4): 903–910. doi:10.1099/ijs.0.024877-0. PMID 20495028.
81. ↑ Sutcliffe, I. C. (2011). "Cell envelope architecture in the Chloroflexi: A shifting frontline in a phylogenetic turf war". Environmental Microbiology 13 (2): 279–282. doi:10.1111/j.1462-2920.2010.02339.x. PMID 20860732. Bibcode: 2011EnvMi..13..279S.
82. ↑ 82.0 82.1 Stackebrandt, E.; Rainey, F. A.; Ward-Rainey, N. L. (1997). "Proposal for a New Hierarchic Classification System, Actinobacteria classis nov". International Journal of Systematic Bacteriology 47 (2): 479–491. doi:10.1099/00207713-47-2-479.
83. ↑ J.P. Euzéby. "List of Prokaryotic names with Standing in Nomenclature: classification of Deinococcus–Thermus". http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus.
84. ↑ Boone, David R., ed (2001). Bergey's Manual® of Systematic Bacteriology. doi:10.1007/978-0-387-21609-6. ISBN 978-1-4419-3159-7.
85. ↑ Cavalier-Smith, T (2002). "The neomuran origin of Archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology 52 (Pt 1): 7–76. doi:10.1099/00207713-52-1-7. PMID 11837318. Bibcode: 2002IJSEM..52....7C.
86. ↑ "List of Prokaryotic names with Standing in Nomenclature—Class Hadobacteria". LPSN. http://www.bacterio.cict.fr/h/hadobacteria.html. Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". Int J Syst Bacteriol 47 (2): 590–2. doi:10.1099/00207713-47-2-590. ISSN 0020-7713. PMID 9103655. http://ijs.sgmjournals.org/cgi/reprint/47/2/590.
87. ↑ Boone DR; Castenholz RW (18 May 2001). Garrity GM. ed. The Archaea and the Deeply Branching and Phototrophic Bacteria. Bergey's Manual of Systematic Bacteriology. 1 (2nd ed.). New York: Springer. pp. 721. British Library no. GBA561951. ISBN 978-0-387-98771-2. https://archive.org/details/bergeysmanualofs00boon/page/721.
88. ↑ "The winds of (evolutionary) change: breathing new life into microbiology". Journal of Bacteriology 176 (1): 1–6. 1994. doi:10.2172/205047. PMID 8282683.

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Prokaryotes: Bacteria classification (phyla and orders)

Domain
Archaea
Bacteria
Eukaryota
(Supergroup
Plant
Hacrobia
Heterokont
Alveolata
Rhizaria
Excavata
Amoebozoa
Opisthokonta

Animal
Fungi)

G-/
OM|

| Terra-/
Glidobacteria
(BV1)|

| Eobacteria|

* Deinococcus–Thermus
* Deinococcales
* Thermales
* Chloroflexi
* Anaerolineales
* Caldilineales
* Chloroflexales
* Herpetosiphonales
* Dehalococcoidales
* Ktedonobacterales
* Thermogemmatisporales
* Thermomicrobiales
* Sphaerobacterales

|

other glidobacteria|

* Thermodesulfobacteria
* thermophiles
* Aquificae
* Thermotogae
* Cyanobacteria

Proteobacteria
(BV2)|

| Alpha|

* Caulobacterales
* Kiloniellales
* Kordiimonadales
* Magnetococcales
* Parvularculales
* Rhizobiales
* Rhodobacterales
* Rhodospirillales
* Rickettsiales
* Sneathiellales
* Sphingomonadales

|

Beta|

* Burkholderiales
* Hydrogenophilales
* Methylophilales
* Neisseriales
* Nitrosomonadales
* Procabacteriales
* Rhodocyclales

Gamma|

* Acidithiobacillales
* Aeromonadales
* Alteromonadales
* Cardiobacteriales
* Chromatiales
* Enterobacterales
* Legionellales
* Methylococcales
* Oceanospirillales
* Orbales
* Pasteurellales
* Pseudomonadales
* Salinisphaerales
* Thiotrichales
* Vibrionales
* Xanthomonadales

Delta|

* Bdellovibrionales
* Desulfarculales
* Desulfobacterales
* Desulfovibrionales
* Desulfurellales
* Desulfuromonadales
* Myxococcales
* Syntrophobacterales
* Syntrophorhabdales

Epsilon|

* Campylobacterales
* Nautiliales

Zeta|

* Mariprofundales

BV4|

| Spirochaetes|

* Spirochaetes

|

Sphingobacteria
(FCB group)|

* Fibrobacteres
* Chlorobi
* Chlorobiales
* Ignavibacteriales
* Bacteroidetes
* Bacteroidales
* Cytophagales
* Flavobacteriales
* Sphingobacteriales

Planctobacteria/
(PVC group)|

* Chlamydiae
* Lentisphaerae
* Lentisphaerales
* Oligosphaerales
* Victivallales
* Planctomycetes
* Phycisphaerales
* Planctomycetales
* Verrucomicrobia
* Puniceicoccales
* Opitutales
* Chthoniobacterales
* Verrucomicrobiales
* "Poribacteria"

Other GN|

* Acidobacteria
* Acidobacteriales
* Acanthopleuribacterales
* Holophagales
* Solibacterales
* Armatimonadetes
* Armatimonadales
* Chthonomonadales
* Fimbriimonadales
* Caldiserica
* Chrysiogenetes
* Deferribacteres
* Dictyoglomi
* Elusimicrobia
* Fusobacteria
* Gemmatimonadetes
* Nitrospirae
* Synergistetes

G+/
no OM|

| Firmicutes
(BV3)|

| Bacilli|

* Bacillales
* Lactobacillales
* Aphragmobacteria
* Erysipelotrichia
* Erysipelotrichiales
* Mollicutes
* Mycoplasmatales
* Entomoplasmatales
* Anaeroplasmatales
* Acholeplasmatales
* Haloplasmatales

|

Clostridia|

* Clostridiales
* Halanaerobiales
* Thermoanaerobacteriales
* Natranaerobiales
* Negativicutes
* Selenomonadales

Thermolithobacteria|

* Thermolithobacterales

Actinobacteria
(BV5)|

| Actinobacteria|

* Actinomycetales
* Bifidobacteriales

|

Acidimicrobiia|

* Acidimicrobiales

Coriobacteriia|

* Coriobacteriales

Nitriliruptoria|

* Euzebyales
* Nitriliruptorales

Rubrobacteria|

* Gaiellales
* Rubrobacterales
* Thermoleophilales
* Solirubrobacterales

Incertae
sedis|

* †Archaeosphaeroides
* †Eobacterium
* †Leptotrichites

Source: Bergey's Manual (2001–2012). Alternative views: Wikispecies.

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Microbiology: Bacteria

Medical
microbiology|

* infection
* Coley's toxins
* Exotoxin
* Lysogenic cycle
* Pathogenic bacteria
* resistance

Biochemistry
and ecology|

| Oxygen
preference|

* Aerobic
* Obligate
* Anaerobic
* Facultative
* Obligate
* Microaerophile
* Nanaerobe
* Aerotolerant

|

Other|

* Extremophile
* Human flora
* Gut
* Lung
* Mouth
* Skin
* Vaginal (In pregnancy)
* Placental
* Uterine
* Salivary
* Microbial metabolism
* Nitrogen fixation
* Microbial ecology
* Primary nutritional groups
* Substrate preference
* Lipophilic
* Saccharophilic

Shape|

* Bacterial cellular morphologies
* Coccus
* Diplococcus
* Bacillus
* Coccobacillus
* Spiral

Structure|

| Cell
envelope|

* Cell membrane
* Cell wall: Peptidoglycan
* NAM
* NAG
* DAP
* Gram-positive bacteria only: Teichoic acid
* Lipoteichoic acid
* Endospore
* Gram-negative bacteria only: Bacterial outer membrane
* Porin
* Lipopolysaccharide
* Periplasmic space
* Mycobacteria only: Arabinogalactan
* Mycolic acid

|

Outside
envelope|

* Bacterial capsule
* Slime layer
* S-layer
* Glycocalyx
* Pilus
* Fimbria
* Non-motile bacteria

Composite|

* Biofilm

Taxonomy|

* Bacteria (classifications)
* Bacterial phyla
* Former groupings: Schizomycetes
* Monera
* Prokaryota
* Gracilicutes
* Firmicutes
* Mollicutes
* Mendosicutes

* Book
* Category
* Commons

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