Branching order of bacterial phyla (Genome Taxonomy Database, 2018)

Main article: Bacterial phyla

There are several models of the branching order of bacterial phyla, one of these is the Genome Taxonomy Database (GTDB).

The GTDB is an initiative to establish a standardised microbial taxonomy based on genome phylogeny, primarily funded by an Australian Research Council Laureate Fellowship. The genomes used to construct the phylogeny are obtained from RefSeq and Genbank, and GTDB releases are indexed to RefSeq releases, starting with release 76. Importantly and increasingly, this dataset includes draft genomes of uncultured microorganisms obtained from metagenomes and single cells, ensuring improved genomic representation of the microbial world. All genomes are independently quality controlled using CheckM before inclusion in GTDB.

The GTDB taxonomy is based on genome trees inferred with FastTree from an aligned concatenated set of 120 single copy marker proteins for Bacteria, and with IQ-TREE from a concatenated set of 53 (since RS207; 122 before) marker proteins for Archaea. Additional marker sets are also used to cross-validate tree topologies including concatenated ribosomal proteins and ribosomal RNA genes.

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. ^{[1] [2] [3] [4] [5]}

Phylogeny

Cladogram was taken from GTDB release 10-RS226 (16th April 2025). ^{[6] [7] [8] [9]}

General note:

• The GTDB data only includes domain and phylum names. Any larger groupings are added by Wikipedia editors by matching to known taxonomic names on a best-effort basis.
• GTDB normalizes rank differences by genomic divergence, creating new names. Comments may be added after these names to indicate other names for such clades in literature.
• Due to the directness of conversion, quotations mark for proposed names are not provided.
• The GTDB tree, although provided in a Newick format with a root, should be treated as "effectively unrooted" according to GTDB authors. ^[10] As a corollary, groups that appear paraphyletic on the GTDB tree are not necessarily paraphyletic: for a paraphyletic group with only one descendant group being left out, a re-rooting of the tree can transform it into a monophyletic group.

Archaea

Archaea Nanobdellati "Altarchaeota" "Iainarchaeota" "Micrarchaeota" "Undinarchaeota" "Huberarchaeaota" "Aenigmarchaeota" "Nanohalarchaeota" Nanobdellota "Methanomada" "Hadarchaeota" Methanobacteriota_B "Hydrothermarchaeota" Methanobacteriota Thermoplasmatota Halobacteriota "Proteoarchaeota" "Korarchaeota" "Korarchaeota" Promethearchaeati Promethearchaeota Thermoproteati Thermoproteota

Methanobacteriati

Bacteria

Bacteria

Chloroflexota (incl. Dormibacterota) Patescibacteria Deinococcota Actinomycetota Bacillati Armatimonadota Sysuimicrobiota Vulcanimicrobiota Bacillota "Cyanoprokaryota" Margulisbacteria Cyanobacteriota (incl. Melainabacteria) Thermotogati "Synergistetes" Atribacterota Synergistota "Thermocalda" Dictyoglomota Thermodesulfobiota Coprothermobacterota Lithacetigenota Caldisericota Bipolaricaulota Thermotogota Fusobacteriota Pseudomonadati Muiribacteriota (incl. Riflebacteria, Wallbacteria) Lindowbacteria Mcinerneyibacteriota Babelota Campylobacterota Spirochaetota Goldbacteria Firestonebacteria Ryujiniota Elusimicrobiota Desantisbacteria Aerophobota Ratteibacteria Omnitrophota OLB16 ("Hinthialibacterota") Sumerlaeota Poribacteria Abyssobacteria Hydrogenedentota "Planctobacteria" Planctomycetota Auribacterota Chlamydiota Verrucomicrobiota "FCB group" ⊞ ⊟ RBG-13-66-14 ("Tangaroaeota", Coatesbacteria) Edwardsbacteria Latescibacterota Zixibacteria Fermentibacterota Orphanbacterota Arandabacterota Joyebacterota Krumholzibacteriota Eisenbacteria Blakebacterota Gemmatimonadota WOR-3 ("Hydrothermota") Cloacimonadota Fibrobacterota Marinisomatota Calditrichota Zhuqueibacterota Chlorobiota AABM5-125-24 ("Electryoneota") Bacteroidota "Proteobacteria/pseudomonadota s.l" ⊞ ⊟ Acidobacteriota Desulfobacterota_E ("Deferrimicrobiota") Desulfobacterota_C ("Deferrisomatota") FEN-1099 ("Lernaellota") Desulfobacterota_B ("Binatota") Myxococcota Schekmanbacteria Moduliflexota Nitrospinota Spongiamicota Tectomicrobia Methylomirabilota Nitrospirota Desulfobacterota Bdellovibrionota "Aquificida" Desulfobacterota_G ("Syntrophorhabdota") ?SZUA-79 (Acidulidesulfobacterales", "Acidulodesulfobacteriota" sic) Desulfobacterota_D ("Dadabacteria") Calescibacterota ("Calescamantes") Thermosulfidibacterota Aquificota Nitrospirota_A ("Leptospirillia", "Leptospirillaeota") Desulfovibrionales {Desulfobacterota_I} SAR324 ("Lambdaproteobacteria") "Oligoflexaeota" Chrysiogenota (incl. Deferribacterota) Pseudomonadota (s.s.)

See also

• Branching order of bacterial phyla (Woese, 1987)
• Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
• Branching order of bacterial phyla after ARB Silva Living Tree
• Branching order of bacterial phyla (Ciccarelli et al., 2006)
• Branching order of bacterial phyla (Battistuzzi et al.,2004)
• Branching order of bacterial phyla (Gupta, 2001)
• Branching order of bacterial phyla (Cavalier-Smith, 2002)

External links

• Genome Taxonomy Database

References

1. 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.
2. 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.
3. 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.
4. 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 . ISSN   1087-0156. PMC   7801254 . PMID   32690973.
5. 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.
6. "GTDB release 10-RS226". Genome Taxonomy Database . Retrieved 1 May 2025.
7. "ar53_r226.sp_label". Genome Taxonomy Database . Retrieved 1 May 2025.
8. "bac120_r226.sp_label". Genome Taxonomy Database . Retrieved 1 May 2025.
9. "Taxon History". Genome Taxonomy Database . Retrieved 1 May 2025.
10. Parks, Donovan (20 January 2025). "Root of bacterial tree?". GTDB Forum. The GTDB reference tree should be treated as unrooted.