List of bacterial orders

Last updated

This article lists the orders of the Bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [1] and National Center for Biotechnology Information (NCBI) [2] and the phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project. [3]

Contents

Phylogeny

National Center for Biotechnology Information (NCBI) taxonomy was initially used to decorate the genome tree via tax2tree. The 16S rRNA-based Greengenes taxonomy is used to supplement the taxonomy particularly in regions of the tree with no cultured representatives. List of Prokaryotic names with Standing in Nomenclature (LPSN) is used as the primary taxonomic authority for establishing naming priorities. Taxonomic ranks are normalised using phylorank and the taxonomy manually curated to remove polyphyletic groups. [4] [5] [6] [7] [8]

Cladogram was taken from GTDB release 09-RS220 (24 April 2024). [9] [10] [11]

Bacteria
Chloroflexae

Chloroflexota

Bacillati
Firmicutes

Bacillota G

Bacillota E

Bacillota s.s.

"Desulfotomaculota" (Bacillota B)

"Selenobacteria" (Bacillota C)

Bacillota D

"Halanaerobiaeota" (Bacillota F)

Bacillota A

"Actinobacteriobiontes"

Actinomycetota

"Pseudomonadati"

Kingdom Bacillati

Phylum Chloroflexota

Phylogeny of Chloroflexota [9] [10] [11]

Phylum "Sysuimicrobiota"

Phylum Armatimonadota

Phylogeny of Armatimonadota [9] [10] [11]
"Heboniibacteriia"

"Heboniibacterales"

"Zipacnadia"

"Zipacnadales"

Abditibacteriia

Abditibacteriales

HRBIN17

HRBIN17

UBA5829

UBA5829

Fimbriimonadia

Fimbriimonadales

Chthonomonadetes

Chthonomonadales

Armatimonadia

Armatimonadales

Phylum Vulcanimicrobiota

Phylogeny of Vulcanimicrobiota [9] [10] [11]
"Xenobia"

"Xenobiales"

Vulcanimicrobiia

Clade Firmicutes

Firmicutes incertae sedis

Phylum Bacillota G

  • Class Limnochordia Watanabe, Kojima & Fukui 2015
  • Class "Hydrogenisporia" Pallen, Rodriguez-R & Alikhan 2022

Phylum Bacillota E

Phylogeny of Bacillota E [9] [10] [11]
UBA3575

UBA3575

Thermaerobacteria

Thermaerobacterales

Symbiobacteriia

Symbiobacteriales

Sulfobacillia

Sulfobacillales

  • Class UBA3575
    • "Candidatus Acetocimmeria" Smith et al. 2021 {UBA3575: UBA3575}
  • Class Thermaerobacteria Chuvochina et al. 2024
  • Class Symbiobacteriia Chuvochina et al. 2024
  • Class Sulfobacillia Chuvochina et al. 2024

Phylum "Selenobacteria"

Phylogeny of Selenobacteria [9] [10] [11]

Phylum "Desulfotomaculota"

Phylogeny of Desulfotomaculota [9] [10] [11]

Phylum Bacillota D

Phylogeny of Bacillota D [9] [10] [11]
"Proteinivoracia"

"Proteinivoracales"

Natranaerobiia

Natranaerobiales

"Dethiobacteria"

SKNC01

"Dethiobacterales"

  • Class "Proteinivoracia"
  • Class "Dethiobacteria" Sorokin & Merkel 2022
    • "Candidatus Contubernalis" corrig. Zhilina et al. 2005 {SKNC01: SKNC01}
    • "Dethiobacterales" Sorokin & Merkel 2022
  • Class Natranaerobiia Chuvochina et al. 2024

Phylum "Halanaerobiaeota"

Phylogeny of Halanaerobiia [9] [10] [11]

Phylum Bacillota A

Phylogeny of Bacillota A [9] [10] [11]

Phylum Mycoplasmatota

Phylogeny of Mycoplasmatota [9] [10] [11]

Phylum "Bacillota"

Phylogeny of Bacillota [9] [10] [11]

Phylum Actinomycetota

Phylogeny of Actinomycetota [9] [10] [11]

Clade Cyanoprokaryota

Phylum "Margulisiibacteriota"

Phylogeny of Margulisiibacteriota [9] [10] [11]

Phylum "Cyanobacteriota"

Phylogeny of Cyanobacteriota [9] [10] [11]

Kingdom Thermotogati

Phylum Atribacterota

Phylum Synergistota

Phylum "Zhurongbacterota"

Phylum Dictyoglomerota

Phylum "Thermodesulfobiota"

Phylum Coprothermobacterota

Phylum "Lithacetigenota"

Phylum Caldisericota

Phylum Thermotogota

Phylogeny of Thermotogota [9] [10] [11]

Clade Candidate Phyla Radiation

Phylum "Elulota"

Phylogeny of Patescibacteria [9] [10] [11]

"Wirthbacteria" (CG2-30-54-11)

"Microgenomates"

"Dojkabacteria"

"Katanobacteria"

"Microgenomatia"

"Woykebacterales"

"Curtissbacterales"

"Daviesbacterales"

"Roizmanbacterales" (UBA1406)

"Gottesmanbacterales" (UBA10105)

"Levybacterales"

GWA2-44-7

"Chazhemtobacteriales"

"Shapirobacterales" (UBA12405)

cluster
"Gracilibacteria"
"Absconditabacteria"

BD1-5

"Absconditabacterales"

"Gracilibacteria"

"Abawacabacterales" (RBG-16-42-10)

"Peregrinibacterales" (UBA1369)

"Fallacibacteriales" (DOLZORAL124_38_8; UBA4473)

"Peribacterales"

cluster
"Parcubacteria"

"Doudnabacteria"

"Andersenbacteria"

"Torokbacteria" (GCA-2792135)

ABY1

"Kerfeldbacterales" (SBBC01)

"Jacksonbacterales" (UBA9629)

"Komeilibacterales" (UBA1558)

"Kuenenbacterales" (UBA2196)

"Veblenbacterales"

"Uhrbacterales" (GWA2-46-9)

"Magasanikbacterales"

"Buchananbacterales"

"Falkowbacterales"

"Moisslbacterales" (UBA2591)

"Paceibacteria"

"Moranbacterales"

UBA6257

"Spechtbacterales"

"Terrybacterales"

"Parcunitrobacterales" (GWA2-38-13b)

"Portnoybacterales"

"Paceibacterales"

"Azambacterales" (UBA10092)

"Yanofskybacterales" (2-02-FULL-40-12)

"Sungbacterales"

"Ryanbacterales"

"Giovannonibacterales"

"Niyogibacterales"

"Tagabacterales"

UBA9973

cluster

Phylum "Patescibacteria"

Clade

Clade "Fusobacterida"

Phylum "Muiribacteriota"

  • Class "Muiribacteriia" corrig. Chuvochina et al. 2023
    • "Muiribacteriales" corrig. Chuvochina et al. 2023

Phylum "Rifleibacteriota"

  • Class "Ozemibacteria" corrig. Kadnikov et al. 2018 (RIF32/ACD39)
    • "Ozemibacterales" corrig. Kadnikov et al. 2018

Phylum "Macinerneyibacteriota"

  • Class "Macinerneyibacteriia" corrig. Yadav et al. 2020
    • "Macinerneyibacteriales" corrig. Yadav et al. 2020

Phylum Fusobacteriota

Clade

Phylum "Bipolaricaulota"

Phylum Deinococcota

Kingdom Pseudomonadati

Clade

Phylum "Goldiibacteriota"

  • "Candidatus Cellulosimonas" Doud et al. 2020

Phylum Elusimicrobiota

Phylum "Aerophobota"

Phylum "Auribacterota"

Phylogeny of "Auribacterota" [9] [10] [11]
"Tritonobacteria"

"Tritonobacterales"

"Erginobacteria"

"Erginobacterales"

"Ancaeobacteria"

"Ancaeobacterales"

"Auribacteria"

"Auribacterales"

JACPWU01

"Theseobacterales"

Phylum "Omnitrophota"

Phylogeny of Omnitrophota [9] [10] [11]

Clade Spirochaetobacteriobiontes

Phylum "Babelota"

  • Class "Babeliae" (sic) Yeoh et al. 2016 (TM6)

Phylum Spirochaetota

Phylogeny of Spirochaetota [9] [10] [11]
"Leptospirae"
Leptospiria
"Euspirochaetae"

Clade Planctobacteria

Phylum Planctomycetota

Phylogeny of Planctomycetota [9] [10] [11]

Phylum Chlamydiota

Phylum Verrucomicrobiota

Phylogeny of Verrucomicrobiota [9] [10] [11]

Clade

Phylum "Saltatorellota"

  • Class "Saltatorellae" Wiegand et al. 2019

Phylum "Hinthialibacterota"

  • Class "Hinthialibacteria" Williams et al. 2022
    • "Hinthialibacterales" Williams et al. 2022 (OLB16)

Phylum "Sumerlaeota"

  • Class "Sumerlaeia" Kadnikov et al. 2018

Phylum "Poribacteriota"

Phylum "Hydrogenedentota"

  • Class "Hydrogenedentia" Chuvochina et al. 2023 (NKB19)

Clade FCB group

Phylum "Heilongiota"

  • Class "Heilongiia" corrig. Zhang et al. 2022
    •  ?"Heilongiales" Zhang et al. 2022

Phylum "Fidelibacterota"

Phylum "Tianyaibacteriota"

Phylum "Fermentibacterota"

Phylum "Latescibacterota"

Phylum "Effluvivivacota"

  • Family "Effluvivivacaceae" corrig. Su et al. 2024 (VGIX01)

Phylum "Krumholzibacteriota"

Phylum Gemmatimonadota

Phylogeny of Gemmatimonadota [9] [10] [11]

Phylum "Hydrothermota"

Phylogeny of Hydrothermota [9] [10] [11]
  • Class "Stahliibacteriia" (UBA3073)
  • Class "Hydrothermia" Chuvochina et al. 2019 ex Chuvochina et al. 2023
    • "Hydrothermales" Chuvochina et al. 2019 ex Chuvochina et al. 2023 (EM3)
    • "Caldipriscales" Pallen, Rodriguez-R & Alikhan 2022 [LBFQ01]

Phylum "Cloacimonadota"

  • Class "Cloacimonadia" Williams et al. 2021 ex Chuvochina et al. 2023
    • "Candidatus Celaenobacter" Williams et al. 2021 {JGIOTU-2: JGIOTU-2}
    • "Cloacimonadales" Williams et al. 2021 ex Chuvochina et al. 2023 (WWE1)

Phylum Fibrobacterota

Phylogeny of Fibrobacterota [9] [10] [11]

Phylum "Electryoneota"

  • Class "Electryoneia" Williams et al. 2022
  • Class AABM5-125-24
  • Class "Tariuqbacteria" Vigneron, Vincent & Lovejoy 2023

Phylum "Marinisomatota"

Phylum Calditrichota

  • Class Calditrichia Kublanov et al. 2022

Phylum "Cosmopoliota"

  • Class "Cosmopolitia" (sic) Zhang et al. 2023

Phylum "Zhuqueibacterota"

Phylogeny of "Zhuqueibacterota" [9] [10] [11]

Phylum Bacteroidota

Phylogeny of Bacteroidota [9] [10] [11]

Clade Proteobacteria

Phylum "Canglongiota"

Phylum Acidobacteriota

Phylogeny of Acidobacteriota [9] [10] [11]

Phylum "Moduliflexota"

  • Class "Moduliflexia" Sekiguchi et al. 2015 (KSB3)

Phylum "Methylomirabilota"

Phylum "Tectimicrobiota"

  • Class "Entotheonellia" Chuvochina et al. 2023

Phylum Nitrospinota

  • Class Nitrospinia Lucker et al. 2022

Phylum Nitrospirota

Phylogeny of Nitrospirota [9] [10] [11]

Phylum SAR324

Phylum Bdellovibrionota

Phylogeny of Bdellovibrionota [9] [10] [11]

Phylum "Binatota"

  • Class "Binatia" Chuvochina et al. 2019 ex Chuvochina et al. 2023
    • "Binatales" Chuvochina et al. 2019 ex Chuvochina et al. 2023

Phylum "Deferrisomatota"

Phylum "Lernaellota"

Phylum Myxococcota

Phylogeny of Myxococcota [9] [10] [11]
  • Class "Kuafubacteriia" corrig. Li et al. 2023
  • Class Myxococcia Waite et al. 2020
    • Myxococcales Tchan, Pochon & Prévot 1948 [Archangiales; "Angiobacteriales"; "Angiococcales"] (fruiting gliding bacteria)
  • Class Bradymonadia corrig. Chuvochina et al. 2024
  • Class Polyangiia corrig. Waite et al. 2020

Phylum "Nitrosediminicolota"

Phylum "Deferrimicrobiota"

Phylum Thermodesulfobacteriota

Phylogeny of Thermodesulfobacteriota [9] [10] [11]

Phylum Desulfobacterota G

Phylum "Dadaibacteriota"

  • Class "Dadabacteria" (sic) Hug et al. 2016 [CSP1-2]

Phylum "Acidulodesulfobacteriota"

  • Class "Acidulodesulfobacteriia" (sic) Pallen, Rodriguez-R & Alikhan 2022 [SZUA-79]

Phylum Chrysiogenota

Phylum Deferribacterota

Phylum Thermosulfidibacterota

  • Class Thermosulfidibacteria Cavalier-Smith 2020 ex Chuvochina et al. 2024

Phylum Aquificota

Phylogeny of Aquificota [9] [10] [11]

Phylum "Calescibacteriota"

  • Class "Calescibacteriia" Chuvochina et al. 2023 (EM19)

Phylum Campylobacterota_A

Phylum Campylobacterota

Phylogeny of Campylobacterota [9] [10] [11]

Phylum "Leptospirillaeota"

  • Class "Leptospirillia" Chuvochina et al. 2023

Phylum Pseudomonadota

Phylogeny of Pseudomonadota [9] [10] [11]
"Caulobacteria"

Holosporales A

Rickettsiales A

Holosporales

Paracaedibacterales

"Caulobacteridae" cont'd

"Mariprofundia"

Mariprofundales

Magnetococcia

Magnetococcales

"Pseudomonadia"
"Neisseriidae"

"Tethybacterales"

Burkholderiales

"Pseudomonadidae"

"Thioglobales"

"Comchoanobacterales"

"Magnimaribacterales"

Pseudomonadales A

Cardiobacteriales

"Chromatiae"

"Enterobacteriae"

Phylogeny of "Caulobacteridae" [9] [10] [11]
Phylogeny of "Pseudomonadidae" [9] [10] [11]

List of Candidate Phyla

See also

References

  1. J.P. Euzéby. "Bacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-06-27.
  2. Sayers; et al. "Bacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.
  3. All-Species Living Tree Project. "16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database . Retrieved 2020-08-20.
  4. Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. bioRxiv   10.1101/256800 . doi:10.1038/nbt.4229. PMID   30148503. S2CID   52093100.
  5. Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv   10.1101/771964 . doi:10.1038/s41587-020-0501-8. PMID   32341564. S2CID   216560589.
  6. Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi: 10.1093/bioinformatics/btz848 . PMC   7703759 . PMID   31730192.
  7. Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. 39 (1): 105–114. doi: 10.1038/s41587-020-0603-3 . PMC   7801254 . PMID   32690973.
  8. Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi: 10.1038/s41587-020-0718-6 . PMC   8041624 . PMID   33169036.
  9. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 "GTDB release 09-RS220". Genome Taxonomy Database . Retrieved 10 May 2024.
  10. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 "bac120_r220.sp_labels". Genome Taxonomy Database . Retrieved 10 May 2024.
  11. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2024.