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Taxonomy browser (Bacteria)

Bacteria

Taxonomy ID: 2 (for references in articles please use NCBI:txid2)
current name
Bacteria Woese et al. 2024 in [Göker M & Oren A (2024)]
homotypic synonym:
"Bacteria" Woese et al. 1990 in [Woese CR et al. (1990)]
Genbank common name: eubacteria
NCBI BLAST name: bacteria
Rank: superkingdom
Genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Other names:
heterotypic synonym
"Bacteria" Cavalier-Smith 1987, effective name 1) in [Cavalier-Smith T (1987)]
heterotypic synonym
"Bacteriobiota" Luketa 2012, effective name 2) in [Luketa S (2012)]
in-part
Monera
in-part
Procaryotae
in-part
Prokaryota
in-part
Prokaryotae
in-part
prokaryote
in-part
prokaryotes
blast name
bacteria
Lineage( full )
cellular organisms
   Entrez records   
Database name Subtree links Direct links
Nucleotide 103,020,541 24
Protein 1,019,169,054 29,892
Structure 72,124 1
Genome 36,976 1
Popset 72,570 12,481
Conserved Domains 22,616 10,120
GEO Datasets 134,309 2,236
PubMed Central 1,357,369 -
Gene 25,329,525 -
SRA Experiments 2,853,805 1,969
GEO Profiles 904,754 -
Protein Clusters 942,125 11,385
Identical Protein Groups 583,974,295 29,841
BioProject 158,970 718
BioSample 4,212,355 1,840
Assembly 2,135,492 -
Genetic Testing Registry 7 -
PubChem BioAssay 143,679 717
Taxonomy 558,970 1

Notes:

Comments and References:
Göker M & Oren A (2024), PubMed: abstract
Göker, M., and Oren, A. "Valid publication of names of two domains and seven kingdoms of prokaryotes." Int. J. Syst. Evol. Microbiol. (2024) 74(1):006242.
Woese CR et al. (1990), doi: 10.1073/pnas.87.12.4576, PubMed: abstract
Woese, C.R., Kandler, O., and Wheelis, M.L. "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya." Proc. Natl. Acad. Sci. USA (1990) 87(12):4576-4579.
Cavalier-Smith T (1987), PubMed: abstract
Cavalier-Smith, T. "The origin of eukaryotic and archaebacterial cells." Ann. N.Y. Acad. Sci. (1987) 503(1):17-54.
Luketa S (2012)
Luketa, S. "New views on the megaclassification of life." Protistology (2012) 7(4):218-237.
Bacteria
When Carl Woese first set forth the three-domain classification of life, he proposed the names "Archaebacteria" and "Eubacteria" for the two prokaryotic domains. These were replaced with the names "Archaea" and "Bacteria" in Woese et al. (1990). The taxonomic name "Bacteria" refers only to the eubacteria. The informal name "bacteria" is occasionally used loosely in the literature to refer to all of the prokayrotes, and care should be taken to interpret it's meaning in any particular context.
Achenbach-Richter L et al. (1987)
Achenbach-Richter, L., Gupta, R., Stetter, K.O., and Woese, C.R. "Were the original eubacteria thermophiles?" Syst. Appl. Microbiol. (1987) 9:34-39.
Christensen H et al. (2000)
Christensen, H., Angen, O., Mutters, R., Olsen, J.E., and Bisgaard, M. "DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA." Int. J. Syst. Evol. Microbiol. (2000) 50:1095-1102.
Christensen H et al. (2001)
Christensen, H., Bisgaard, M., Frederiksen, W., Mutters, R., Kuhnert, P., and Olsen, J.E. "Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision)." Int. J. Syst. Evol. Microbiol. (2001) 51:2221-2225.
Clayton RA et al. (1995)
Clayton, R.A., Sutton, G., Hinkle, P.S. Jr, Bult, C., and Fields, C. "Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa." Int. J. Syst. Bacteriol. (1995) 45:595-599.
Dalevi D et al. (2001)
Dalevi, D., Hugenholtz, P., and Blackall, L.L. "A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data." Int. J. Syst. Evol. Microbiol. (2001) 51:385-391.
Euzeby JP (1997b)
Euzeby, J.P. "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet." Int. J. Syst. Bacteriol. (1997) 47:590-592.
Göker M et al. (2022), doi:10.1099/ijsem.0.005754
Göker, M., Moore, E.R.B., Oren, A., and Trujillo, M.E. "Status of the SeqCode in the International Journal of Systematic and Evolutionary Microbiology." Int. J. Syst. Evol. Microbiol. (2022) 72(12):005754.
Gurtler V & Mayall BC (2001)
Gurtler, V., and Mayall, B.C. "Genomic approaches to typing, taxonomy and evolution of bacterial isolates." Int. J. Syst. Evol. Microbiol. (2001) 51:3-16
Haeckel EH (1894)
Haeckel, E.H.: Systematische Phylogenie der Protisten und Planzen. (1894) I.G. Reimer, Berlin. p. 40.
Hansmann S & Martin W (2000)
Hansmann, S., and Martin, W. "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis." Int. J. Syst. Evol. Microbiol. (2000) 50:1655-1663.
Keswani J & Whitman WB (2001)
Keswani, J., and Whitman, W.B. "Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes." Int. J. Syst. Evol. Microbiol. (2001) 51:667-678.
Moore LV et al. (1994b)
Moore, L.V., Bourne, D.M., and Moore, W.E. "Comparative distribution and taxonomic value of cellular fatty acids in thirty-three genera of anaerobic gram-negative bacilli." Int. J. Syst. Bacteriol. (1994) 44:338-347.
Murray RG & Schleifer KH (1994)
Murray, R.G., and Schleifer, K.H. "Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes." Int. J. Syst. Bacteriol. (1994) 44(1):174-176.
Palys T et al. (1997)
Palys, T., Nakamura, L.K., and Cohan, F.M. "Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data." Int. J. Syst. Bacteriol. (1997) 47:1145-1156.
Stackebrandt E et al. (2002)
Stackebrandt, E., Frederiksen, W., Garrity, G.M., Grimont, P.A., Kampfer, P., Maiden, M.C., Nesme, X., Rossello-Mora, R., Swings, J., Truper, H.G., Vauterin, L., Ward, A.C., and Whitman, W.B. "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology." Int. J. Syst. Evol. Microbiol. (2002) 52:1043-1047.
Sutcliffe IC et al. (2020), other link:https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pmc/articles/PMC7657488/
Sutcliffe, I.C., Dijkshoorn, L., Whitman, W.B., Executive Board OBOTI. "Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote." Int. J. Syst. Evol. Microbiol. (2020) 70(7):4416-4417.
Tindall BJ (1999b)
Tindall, B.J. "Proposals to update and make changes to the Bacteriological Code." Int. J. Syst. Bacteriol. (1999) 49:1309-1312. [No abstract available.]
Tindall BJ (1999c)
Tindall, B.J. "Misunderstanding the Bacteriological Code." Int. J. Syst. Bacteriol. (1999) 49:1313-1316.
Tindall BJ (1999d)
Tindall, B.J. "Proposal to change Rule 18a, Rule 18f and Rule 30 to limit the retroactive consequences of changes accepted by the ICSB." Int. J. Syst. Bacteriol. (1999) 49:1321-1322. [No abstract available.]
Tindall BJ (1999e)
Tindall, B.J. "Proposal to change the Rule governing the designation of type strains deposited under culture collection numbers allocated for patent purposes." Int. J. Syst. Bacteriol. (1999) 49:1317-1319. [No abstract available.]
Truper HG (1994)
Truper, H.G., "Taxonomic notes: Names for higher taxa and their impact on the Code of Nomenclature of Bacteria." Int. J. Syst. Bacteriol. (1994) 368-369. [No PubMed record available.]
Viale AM et al. (1994)
Viale, A.M., Arakaki, A.K., Soncini, F.C., and Ferreyra, R.G. "Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons." Int. J. Syst. Bacteriol. (1994) 44:527-533.
Winker S & Woese CR (1991)
Winker, S., and Woese, C.R. "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics." Syst. Appl. Microbiol. (1991) 14:305-310.
Woese CR & Fox GE (1977)
Woese, C.R., and Fox, G.E. "Phylogenetic structure of the prokaryotic domain: the primary kingdoms." Proc. Natl. Acad. Sci. U S A (1977) 74:5088-5090.
Woese CR et al. (1985)
Woese, C.R., Stackebrandt, E., Macke, T.J., and Fox, G.E. "A phylogenetic definition of the major eubacterial taxa." Syst. Appl. Microbiol. (1985) 6:143-151.
Xu HX et al. (2000)
Xu, H.X., Kawamura, Y., Li, N., Zhao, L., Li, T.M., Li, Z.Y., Shu, S., and Ezaki, T. "A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube." Int. J. Syst.Evol. Microbiol. (2000) 50:1463-1469.
Young JM (2000)
Young, J.M. "Suggestions for avoiding on-going confusion from the Bacteriological Code." Int. J. Syst. Evol. Microbiol. (2000) 50:1687-1689. [No abstract available.]
Young JM (2001)
Young, J.M. "Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy." Int. J. Syst. Evol. Microbiol. (2001) 51:945-953.

External Information Resources (NCBI LinkOut)

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9 records from this provider taxonomy/phylogenetic NCBI taxonomy bookmarks
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Bacteria taxonomy/phylogenetic Ocean Biogeographic Information System
Eubacteria taxonomy/phylogenetic Tree of Life
2 records from this provider taxonomy/phylogenetic TreeBase
UCMP taxonomy/phylogenetic UCMP phylogeny exhibit
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Information from sequence entries

Organism modifiers

To hide organism modifiers click here
strain
GH443 [1] HD-1 [6 12 2 8537 567 3 24674 24 1] IFAM 1493 [1] IFAM 2074 [1]
IFAM 3211 [1] IFAM 3215 [1] IFAM 3359 [3] PB90-2 [1]
UGO163/26 [1 1] XB45 [2] soil clone, member of a novel phyla [1] soil clone, member of a novel phylum [1]
soil clone, p1 anctomycetes related [6] soil clone,member ov a novel phylum [1] soil clone,novel line of descented [1] soil clone,p1 anctomycetes related [6]
soil clone,p1 anctomycetes related member [1]
isolate
1-140 C12 [2] 1-140 C23 [2] 1-140 C39 [2] 1-140 C40 [2]
1-140 C6 [2] 1-140 C7 [2] 1-420 C13 [1] 1-420 C25 [1]
1-420 C26 [1] 1-420 C3 [1] 1-420 C55 [1] 1-700 C1 [2]
1-700 C10 [2] 1-700 C11 [2] 1-700 C14 [2] 1-700 C19 [1]
1-700 C39 [1] 1-700 C4 [2] 1-700 C40 [2] 1-700 C41 [2]
1-700 C46 [2] 1-700 C7 [2] 1-700 C9 [2] 1011 [7 10 5 1 7]
10a [7 232 1 4061 6] 1111 [1 6 7 2 6] 11W109 [1] 11W110 [1]
11W111 [1] 11W112 [1] 11a [9 374 4 5809 8] 11w103 [1]
12a [8 221 2 4053 8] 13a [8 206 3 4043 7] 1411 [6 5 6] 14a [8 180 4 4028 7]
15a [5 200 1 4037 4] 1611 [5 4 1 5] 16a [7 237 3 4044 6] 17a [8 247 4 4053 7]
1911 [4 5 4] 19a [5 212 3 4034 5] 2-100 C1.12 [1] 2-100 C1.14 [1]
2-100 C1.2 [1] 2-100 C1.5 [2] 2-100 C1.8 [2] 2-100 C1.9 [2]
2-100 C2 [2] 2-100 C4 [2] 2-400 C2.16 [2] 2-400 C2.23 [2]
2-400 C2.29 [2] 2-400 C2.3 [2] 2-400 C2.9 [2] 2-400 C2/2.11 [2]
2-400 C2/2.19 [2] 2011 [1 7 7 1 7] 211 [43 382 10 5 39] 21a [3 234 3 4049 3]
22a [4 162 4 4059 5] 26a [4 200 2 4034 3] 3011 [5 3 3] 311 [38 265 7 7 36]
3111 [9 8 9] 31a [5 196 5 4040 5] 3311 [1] 33a [5 180 4 4063 4]
34a [3 181 4 4028 3] 35a [6 150 1 4031 4] 3611 [1 75 1 72 1] 3711 [1]
37a [6 796 2 4046 5] 3811 [3 2 1] 38a [5 202 4060 5] 3911 [1 2 1]
39a [2 6247 7806 2] 3c [6 11 4 2 7] 41a [5 167 2 4025 4] 4211 [5 6 6]
42a [7 180 1 4045 6] 4511 [2 44 1 43] 4611 [1 2 1] 4711 [2 2 2]
47a [6 208 4 4120 5] 4811 [1 2 1] 48a [7 422 8 4055 7] 4911 [1]
4A [15 486 2 7 6207 22] 5011 [1 1 1] 511 [30 18 4 29] 5111 [1 1 1]
51a [4 59 2 2 4] 5211 [1] 52a [5 187 1 5] 5311 [1]
53a [1 3 1 2 1] 5411 [1] 54A [4 3 1 3] 5511 [1]
5811 [1] 5911 [2 3 2] 60a [3 3 1 2] 6511 [1]
66A [4 156 1 3] 6711 [1 2 2] 6811 [2] 6911 [1]
7011 [1] 7087 [1 1 1] 7211 [1] 7911 [1]
8011 [1] 811 [16 16 4 1 15] 8211 [1] 8511 [1]
8911 [1] 8a [10 168 4 4069 10] 911 [16 14 4 1 16] A2 [2 46 2 6495 3 23 14904 71]
A3 [4 42 2782 14 12786 189] A6 [1 21 1336 13 1663 32] A7 [1 21 389 10 9315 16] A8 [2 19 1633 13 15379 35]
AAN036 [1] ANO011 [1] AW10 [1] AW2 [1 3 1 2]
AW22 [1] AW23 [1] AW5 [1 2 2] AW6 [1]
AW9 [1] Boom-3m-01 [1] Boom-3m-02 [1] Boom-3m-03 [1]
Boom-3m-04 [1] Boom-3m-05 [1] Boom-3m-06 [1] Boom-3m-07 [1]
Boom-3m-08 [1] Boom-3m-09 [1] Boom-3m-11 [1] Boom-3m-12 [1]
Boom-3m-14 [1] Boom-7m-01 [1] Boom-7m-02 [1] Boom-7m-03 [1]
Boom-7m-04 [1] Boom-7m-05 [1] Boom-7m-06 [1] Boom-7m-07 [1]
Boom-7m-08 [1] Boom-7m-10 [1] Boom-7m-11 [1] Boom-7m-12 [1]
Boom-7m-13 [1] Boom-7m-14 [1] Boom-7m-15 [1] Boom-7m-16 [1]
Boom-7m-21 [1] Boom-7m-22 [1] Boom-7m-23 [1] Boom-7m-24 [1]
Boom-7m-25 [1] C2203 [1] Crater Lake isolate 11C1 [1] Crater Lake isolate 12C1 [1]
Crater Lake isolate 13C1 [1] Crater Lake isolate 29C1 [1] Crater Lake isolate 75C4 [1] HB1-1 [1]
HB1-2 [1 1 1] HB1-3 [1] HB1-4 [1] HB1-5 [1 1 1]
Lake Bogoria isolate 10B1 [1] Lake Bogoria isolate 24B1 [1] Lake Bogoria isolate 25B1 [1] Lake Bogoria isolate 64B4 [1]
Lake Bogoria isolate 65B4 [1] Lake Bogoria isolate 66B4 [1] Lake Bogoria isolate 69B4 strain type strain: 69B4 [1] of Cellulomonas bogoriensis Lake Bogoria isolate 8B1 [1]
Lake Bogoria isolate 9B1 [1] Lake Bogoria isolate WB2 [1] Lake Bogoria isolate WB3 [1] Lake Bogoria isolate WB4 [1]
Lake Bogoria isolate WB5 [1] Lake Elmenteita isolate 2E1 [1] Lake Elmenteita isolate 35E2 [1] Lake Elmenteita isolate 3E1 [1]
Lake Elmenteita isolate 44E3 [1] Lake Elmenteita isolate 45E3 [1] Lake Elmenteita isolate WE1 [1] Lake Elmenteita isolate WE2 [1]
Lake Elmenteita isolate WE4 [1] Lake Elmenteita isolate WE5 [1] Lake Magadi isolate 21M1 [1] Lake Magadi isolate 27M1 [1]
Lake Nakuru isolate 17N1 [1] Lake Nakuru isolate 18N1 [1] Lake Nakuru isolate 19N1 [1] Lake Nakuru isolate 20N1 [1]
Lake Nakuru isolate 28N1 [1] Lake Nakuru isolate 52N3 [1] Lake Nakuru isolate WN16 [1] Lake Natron isolate 103NT4 [1]
Lake Natron isolate 105NT4 [1] Lake Natron isolate 97NT4 [1] Little Lake Magadi isolate 95LM4 [1] Little Lake Naivasha isolate 14LN1 [1]
PAN031 [1] PNO019 [1] R2102 [1] R2105 [1]
T25 [1 3 1 1] T3 [1 8 367 13 2690 245] T41 [2 6 2 2 1] T5811 [1]
TM1 [1 1] TM10 [1] TM13 [1] TM18 [1]
TM2 [1] TM200 [1] TM21 [1] TM22 [1]
TM255 [1] TM29 [1] TM44 [3] TM5 [1]
TM6 [2 1] TM7 [1] TM72 [1] TM76 [1]
TM84 [1] clone group G1 [1] clone group G10 [1] clone group G11 [1]
clone group G12 [1] clone group G13 [1] clone group G14 [1] clone group G15 [1]
clone group G16 [1] clone group G17 [1] clone group G18 [1] clone group G19 [1]
clone group G2 [1] clone group G20 [1] clone group G21 [1] clone group G22 [1]
clone group G23 [1] clone group G24 [1] clone group G25 [1] clone group G26 [1]
clone group G27 [1] clone group G28 [1] clone group G29 [1] clone group G3 [1]
clone group G30 [1] clone group G31 [1] clone group G32 [1] clone group G33 [1]
clone group G34 [1] clone group G35 [1] clone group G36 [1] clone group G37 [1]
clone group G38 [1] clone group G39 [1] clone group G4 [1] clone group G40 [1]
clone group G41 [1] clone group G42 [1] clone group G43 [1] clone group G44 [1]
clone group G5 [1] clone group G6 [1] clone group G7 [1] clone group G8 [1]
clone group G9 [1] mark05 [1] mark10 [1] mark13 [1]

Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information.

Reference: How to cite this resource - Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. PubMed: 32761142 PMC: PMC7408187.


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