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

From Wikipedia, the free encyclopedia
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 122 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 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 the website, which uses the GTDB release 05-RS95 (17 July 2020).[6]

Archaea
"DPANN"
 

 
 
"Diapherotrites"
 

 
 

Micrarchaeota

 
 
 
 

 
 
 
 

Aenigmarchaeota

 
 
 

 
 

Nanohaloarchaeota

 
 
 
 

Nanoarchaeota

 
 
 
 
 
 
"Euryarchaeida"
 
 

 
 
 

Hadarchaeota

 
 

""

 
 
 
 
 

""

 
 

"" (Class II Methanogens)

 
 
 
 
"Filarchaeota"

"Thermoproteota"

 
Asgard group

Asgardaeota

 
 
 
 
Bacteria
Terrabacteria
Cyanoprokaryota
 

""

 
 

Cyanobacteria

 
 
 
 
 
 

Armatimonadota

 
 
 

 
 
 

 
 

Chloroflexota

 
 
 
 
 
 

Deinococcota

 
 

Actinobacterota

 
 
 
Firmicutes
��

Firmicutes G

 
 
 

Firmicutes E

 
 
 
 

Negativicutes (Firmicutes C)

 
 

Firmicutes B

 
 
 
 
 

Halanaerobiales (Firmicutes F)

 
 

Firmicutes A

 
 
 
 

Firmicutes D

 
 
 

Fusobacterota

 
 

Bacillota

 
 
 
 
 
 
 
 
 
 
 
Candidate Phyla Radiation

Patescibacteria

 
Thermotogida
 
 
 

 
 

 
 
 
 

Dictyoglomota

 
 
 

Coprothermobacterota

 
 

Caldisericota

 
 
 
 
 
 

Synergistota

 
 
 

 
 

Thermotogota

 
 
 
 
 
Hydrobacteria
 
 

 
 
 

 
 

 
 
 
 
 
 
 
 

 
 

 
 
 

Spirochaetota

 
 
 
 
 

Chrysiogenota

 
 

Deferribacterota

 
 
 
 
 

 
 

Aquificota

 
 
 

Campylobacterota

 
 
 
 
 
"Elusimicrobes"
 
 

 
 
 

 
 

 
 
 
 
 
 

 
 

 
 
 

Elusimicrobota

 
 
 
 
 
Planctobacteria
 

 
 
 

Planctomycetota

 
 
 

 
 
 

Chlamydota

 
 

Verrucomicrobiota

 
 
 
 
 
FCB group
 
 

 
 

Fermentibacteria

 
 
 
 
 

 
 
 

Gemmatimonadota

 
 
 

 
 

 
 
 
 
 
 
 

Zixibacteria

 
 

 
 
 
 
 

 
 

Fibrobacterota

 
 
 
 
 

 
 

Calditrichaeota

 
 
 

Bacteroidota

 
 
 
 
 
 
 
 
 
 

Poribacteria

 
 
 

 
 
 

 
 

 
 
 
 
Proteobacteria
 

Acidobacterota

 
 
 
 
 

Modulibacteria

 
 
 

 
 
 

 
 

Nitrospinota

 
 
 
 
 
 

 
 

Nitrospirota

 
 
 
 
 

Desulfobacterota

 
 
 

Bdellovibrionota

 
 
 
 

 
 

 
 
 
 

Myxococcota

 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 

See also[]

External links[]

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. 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. doi:10.1038/s41587-020-0603-3. ISSN 1087-0156. PMC 7801254. PMID 32690973.
  5. ^ Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, José P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. doi:10.1038/s41587-020-0718-6. PMC 8041624.
  6. ^ Mendler, K; Chen, H; Parks, DH; Hug, LA; Doxey, AC (2019). "AnnoTree: visualization and exploration of a functionally annotated microbial tree of life". Nucleic Acids Research. 47: 4442–4448. doi:10.1093/nar/gkz246. PMC 6511854.
Retrieved from ""