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

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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

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Cladogram was taken from GTDB release 08-RS214 (28th April 2023).[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.

Archaea

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Archaea

Bacteria

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Bacteria

Dormibacterota

Armatimonadota

Eremiobacterota

Firmicutes (Bacillota s.l.)

Bacillota_E

Bacillota_G

Bacillota_F ("Halanaerobiaeota")

Bacillota_B ("Desulfotomaculota")

Bacillota_C ("Selenobacteria")

Bacillota_A

Bacillota_D

Bacillota (s.s.)

"Cyanoprokaryota"

Margulisbacteria

Cyanobacteriota (incl. Melainabacteria)

"Hydrobacteria"
"Proteobacteria/pseudomonadota s.l"
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See also

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References

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  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 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  7. ^ "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  8. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  9. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
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