Taxonomy browser (Bacteria)

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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 name¹⁾ in [Cavalier-Smith T (1987)]

heterotypic synonym

"Bacteriobiota" Luketa 2012, effective name²⁾ 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	108,004,071	24
Protein	1,098,402,597	43,263
Structure	74,333	1
Popset	73,410	12,486
Conserved Domains	22,616	10,120
GEO Datasets	140,441	2,468
PubMed Central	1,416,359	1
Gene	27,762,056	-
SRA Experiments	3,238,961	2,196
GEO Profiles	904,754	-
Protein Clusters	942,125	11,385
Identical Protein Groups	686,703,148	39,606
BioProject	164,703	764
BioSample	4,724,297	2,067
Datasets Genome	2,407,362	-
Genetic Testing Registry	9	-
PubChem BioAssay	148,188	814
Taxonomy	576,085	1

Notes:

1) This taxonomic name has been effectively published but not validly published under the rules of the International Code of Nomenclature of Prokaryotes (Bacteriological Code).
2) This taxonomic name has been effectively published but not validly published under the rules of the International Code of Nomenclature of Prokaryotes (Bacteriological Code).

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://www.ncbi.nlm.nih.gov/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)

LinkOut	Subject	LinkOut Provider
2 records from this provider	taxonomy/phylogenetic	Arctos Specimen Database
Bacteria	taxonomy/phylogenetic	Encyclopedia of life
GOLD: 25 Organisms	organism-specific	Genomes On Line Database
Show Biotic Interactions	taxonomy/phylogenetic	Global Biotic Interactions
Related Immune Epitope Information	gene/protein/disease-specific	Immune Epitope Database and Analysis Resource
Bacteria T. Cavalier-Smith	taxonomy/phylogenetic	Index Nominum Algarum
2 records from this provider	taxonomy/phylogenetic	Integrated Taxonomic Information System
Bacteria	taxonomy/phylogenetic	Lifemap
9 records from this provider	taxonomy/phylogenetic	NCBI taxonomy bookmarks
OMA	taxonomy/phylogenetic	OMA Browser: Orthologous MAtrix
Bacteria	taxonomy/phylogenetic	Ocean Biogeographic Information System
Bacteria \| SeqCode Registry	taxonomy/phylogenetic	SeqCode Registry
Eubacteria	taxonomy/phylogenetic	Tree of Life
2 records from this provider	taxonomy/phylogenetic	TreeBase
UCMP	taxonomy/phylogenetic	UCMP phylogeny exhibit
Bacteria	taxonomy/phylogenetic	World Register of Marine Species
Wikipedia	taxonomy/phylogenetic	iPhylo

Notes:: Groups interested in participating in the LinkOut program should visit the LinkOut home page.
A list of our current non-bibliographic LinkOut providers can be found here.

Information from sequence entries

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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.

Comments and questions to info@ncbi.nlm.nih.gov

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