Taxonomy and Systematics

Systematics may succinctly be described as "the cradle of comparative biology". It encompasses ☞ characterization, ☞ classification, and nomenclature. The term "taxonomy" is often used interchangeably with systematics. It appears to make more sense to regard taxonomy as the domain within systematics that is concerned with classification. As an aspect of systematics, taxonomy thus constitutes a kind of classification that uses names and by doing so is affected by the ☞ rules of nomenclature. Identification is often considered to be a part of taxonomy but may better be regarded as a ☞ separate kind of undertaking that depends on taxonomy.

Information on taxonomy and systematics available at LPSN:

• The page on phylogenetic inference explains the relationship between taxonomic classification and phylogeny and provides hints on the inference, display, and interpretation of phylogenetic trees.
• The LPSN glossary contains definitions and explanations some of which are related to taxonomy.
• List of minimal standards for the description of new taxa and minutes of meetings of Taxonomic Subcommittees of the International Committee on Systematics of Prokaryotes
• Clarification of the relationship between nomenclature and taxonomy
• B.J. Tindall: Misunderstanding the Bacteriological Code
• P.H.A. Sneath & Don J. Brenner: "Official" Nomenclature Lists
• For overall numbers of taxon names please see the LPSN statistics page.
• For the number of species per genus, see the page on the largest genera.
• For the approximate number of taxonomic proposals per country see the page on corresponding authors.

A chronologically sorted selection of publications (which may or may not be endorsed by those responsible for LPSN) on the taxonomy of prokaryotes:

1961-1965

• Anonymous. Recommendations: Subcommittee on Taxonomy of Staphylococci and Micrococci. International Bulletin of Bacteriological Nomenclature and Taxonomy 1965; 15:109-110.
• Cowan ST. PRINCIPLES AND PRACTICE OF BACTERIAL TAXONOMY--A FORWARD LOOK. J Gen Microbiol 1965; 39:143-153.

1981-1985

• Holdeman LV, Cato EP, Moore WE. Taxonomy of anaerobes: present state of the art. Rev Infect Dis 1984; 6:S3-10.

1986-1990

• Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 1987; 37:463-464.
• Grimont PA. Use of DNA reassociation in bacterial classification. Can J Microbiol 1988; 34:541-546.
• Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Systematic and Applied Microbiology 1988; 10:99-100.
• Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433-434.
• Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. J Appl Bacteriol 1988; 64:283-284.

1991-1995

• Canhos VP, Manfio GP, Blaine LD. Software tools and databases for bacterial systematics and their dissemination via global networks. Antonie Van Leeuwenhoek 1993; 64:205-229.
• Kohring LL, Ringelberg DB, Devereux R, Stahl DA, Mittelman MW, White DC. Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria. FEMS Microbiol Lett 1994; 119:303-308.
• STACKEBRANDT (E.) and GOEBEL (B.M.): A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 1994, 44, 846-849.
• Ursing JB, Rossello-Mora RA, Garcia-Valdes E, Lalucat J. Taxonomic Note: A Pragmatic Approach to the Nomenclature of Phenotypically Similar Genomic Groups. International Journal of Systematic Bacteriology 1995; 45:604-604.

1996-2000

• STACKEBRANDT (E.), TINDALL (B.), LUDWIG (W.) and GOODFELLOW (M.): Prokaryotic diversity and systematics. In: J. LENGELER, G. DREWS and H. SCHLEGEL (eds), Biology of the Prokaryotes, G. Thieme, Stuttgart, 1999, pp. 675–720.

2001-2005

• MURRAY (R.G.E.), HOLT (J.G.), KRIEG (N.R.), GARRITY (G.M.), BRENNER (D.J.), STALEY (J.T.), SNEATH (P.H.A.), LUDWIG (W.), KLENK (H.P.), AMANN (R.), SCHLEIFER (K.H.), TRÜPER (H.G.), ZINDER (S.H.), SALYERS (A.A.) and LABEDA (D.P.): Introductory chapters. In: D. R. BOONE, R. W. CASTENHOLZ and G. M. GARRITY (eds), Bergey’s Manual of Systematic Bacteriology. The Archaea and the Deeply Branching and Phototrophic Bacteria, second edition, vol. 1, Springer, New York, 2001, pp. 1-166.
• Christensen H, Bisgaard M, Frederiksen W, Mutters R, Kuhnert P, Olsen JE. 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.
• Lan R, Reeves PR. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol 2001; 9:419-424.
• Young JM. Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 2001; 51:945-953.
• STACKEBRANDT (E.), FREDERIKSEN (W.), GARRITY (G.M.), GRIMONT (P.A.D.), KÄMPFER (P.), MAIDEN (M.C.J.), NESME (X.), ROSSELLO-MORA (R.), SWINGS (J.), TRÜPER (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. International Journal of Systematic and Evolutionary Microbiology 2002, 52, 1043–1047.
• Dellaglio F, Felis GE, Germond JE. Should names reflect the evolution of bacterial species? Int J Syst Evol Microbiol 2004; 54:279-281.
• Owen RJ. Bacterial taxonomics: finding the wood through the phylogenetic trees. Methods Mol Biol 2004; 266:353-383.
• STACKEBRANDT (E.): Will we ever understand? The undescribable diversity of the prokaryotes. Acta Microbiologica et Immunologica Hungarica, 2004, 51, 449-462.
• Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258-6264.
• Rossello-Mora R. Updating prokaryotic taxonomy. J Bacteriol 2005; 187:6255-6257.

2006-2010

• DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072.
• Gevers D, Dawyndt P, Vandamme P, Willems A, Vancanneyt M, Swings J, De Vos P. Stepping stones towards a new prokaryotic taxonomy. Philos Trans R Soc Lond B Biol Sci 2006; 361:1911-1916.
• Maiden MC. Multilocus sequence typing of bacteria. Annu Rev Microbiol 2006; 60:561-588.
• STACKEBRANDT (E.): Defining Taxonomic Ranks. In: DWORKIN, M., FALKOW, S., ROSENBERG, E., SCHLEIFER, K.H. and STACKEBRANDT, E. (eds), The Prokaryotes, Springer, New York, 2006, pp. 29-57.
• STACKEBRANDT (E.) and EBERS (J.): Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 2006, 33, 152–155.
• Zakhia F, de Lajudie P. [Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)]. Can J Microbiol 2006; 52:169-181.
• BUCKLEY (M.) and ROBERTS (R. J.): Reconciling microbial systematics and genomics. American Academy of Microbiology, Washington DC, 2007, pp. 1-10.
• Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188-7196.
• TINDALL (B.J.), SIKORSKI (J.), SMIBERT (R.A.) and KRIEG (K.R.): Phenotypic Characterization and the Principles of Comparative Systematics. In: C.A. REDDY, T.J. BEVERIDGE, J.A. BREZNAK, G. MARZLUF, T.M. SCHMIDT, L.R. SNYDER (editors), Methods for General and Molecular Microbiology, 3rd Edition, ASM Science, Washington (D.C.), 2007, p. 330-393.
• Slabbinck B, De Baets B, Dawyndt P, De Vos P. Towards large-scale FAME-based bacterial species identification using machine learning techniques. Syst Appl Microbiol 2009; 32:163-176.
• Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Systematic and Applied Microbiology 2010; 33:175-182.
• Moore ER, Mihaylova SA, Vandamme P, Krichevsky MI, Dijkshoorn L. Microbial systematics and taxonomy: relevance for a microbial commons. Res Microbiol 2010; 161:430-438.
• Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249-266.

2011-2015

• Bowman JP. Approaches for the characterization and description of novel methanotrophic bacteria. Methods Enzymol 2011; 495:45-62.
• Schumann P. Peptidoglycan structure. In: Rainey FA, Oren A (eds), Taxonomy of Prokaryotes, Academic Press, Chennai, 2011, pp. 101-129.
• Barona-Gomez F, Cruz-Morales P, Noda-Garcia L. What can genome-scale metabolic network reconstructions do for prokaryotic systematics? Antonie Van Leeuwenhoek 2012; 101:35-43.
• Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (Reading) 2012; 158:1005-1015.
• Kämpfer P. Systematics of prokaryotes: the state of the art. Antonie Van Leeuwenhoek 2012; 101:3-11.
• Kämpfer P, Glaeser SP. Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited. Environ Microbiol 2012; 14:291-317.
• Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716-721.
• Sutcliffe IC, Trujillo ME, Goodfellow M. Special Issue on The BISMiS 2011 Prokaryotic Systematics, a vital discipline entering a period of transition. Antonie van Leeuwenhoek 2012; 101:1-2.
• Göker M, Klenk HP. Phylogeny-driven target selection for genome-sequencing (and other) projects. Standards in Genomic Sciences 2013; 8:360-374.
• Kämpfer P, Glaeser SP. Prokaryote Characterization and Identification. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds), The Prokaryotes. Prokaryotic Biology and Symbiotic Associations, fourth edition, vol. 1. Springer, Heidelberg, 2013, pp. 123-147.
• Konstantinidis KT, Stackebrandt E. Defining Taxonomic Ranks. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds), The Prokaryotes. Prokaryotic Biology and Symbiotic Associations, fourth edition, vol. 1. Springer, Heidelberg, 2013, pp. 229-254.
• Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy? Archives of Microbiology 2013; 195:413-418.
• Murphy EC, Frick IM. Gram-positive anaerobic cocci--commensals and opportunistic pathogens. FEMS Microbiol Rev 2013; 37:520-553.
• Marakeby H, Badr E, Torkey H, Song Y, Leman S, Monteil CL, Heath LS, Vinatzer BA. A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature. PLoS One 2014; 9:e89142.
• Meier-Kolthoff JP, Hahnke L, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin A, Chertkov O, Reddy K, Pati A, Ivanova N, Markowitz V, Kyrpides C, Woyke T, Göker M, Klenk HP. Complete genome sequence of DSM 30083^T, the type strain (U5/41^T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Standards in Genomic Sciences 2014; 10:2.
• Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of the G+C content and DNA:DNA hybridization in the genomic age. International Journal of Systematic and Evolutionary Microbiology 2014; 64:352-356.
• Oren A, Garrity GM. Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie Van Leeuwenhoek 2014; 106:43-56.
• Vandamme P, Peeters C. Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 2014; 106:57-65.
• Yarza P, Yilmaz P, Pruesse E, Glockner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rossello-Mora R. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635-645.
• Flandrois JP, Perriere G, Gouy M. leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics 2015; 16:251.
• Hedlund BP, Dodsworth JA, Staley JT. The changing landscape of microbial biodiversity exploration and its implications for systematics. Syst Appl Microbiol 2015; 38:231-236.
• Rossi-Tamisier M, Benamar S, Raoult D, Fournier PE. Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species. Int J Syst Evol Microbiol 2015; 65:1929-1934.
• Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes. Syst Appl Microbiol 2015; 38:217-222.
• Yilmaz P, Yarza P, Rapp JZ, Glockner FO. Expanding the World of Marine Bacterial and Archaeal Clades. Front Microbiol 2015; 6:1524.

2016-2020

• Abdallah RA, Beye M, Diop A, Bakour S, Raoult D, Fournier PE. The impact of culturomics on taxonomy in clinical microbiology. Antonie Van Leeuwenhoek 2017; 110:1327-1337.
• Konstantinidis KT, Rossello-Mora R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399-2406.
• Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, et al. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. Euro Surveill 2017; 22:0.
• Overmann J, Abt B, Sikorski J. Present and future of culturing bacteria. Annual Review of Microbiology 2017; 71:711-730.
• Brown DR. Notice of impending dissolution of inactive Subcommittees on Taxonomy. Int J Syst Evol Microbiol 2018; 68:2102-2103.
• Dallman T, Ashton P, Schafer U, Jironkin A, Painset A, Shaaban S, Hartman H, Myers R, Underwood A, Jenkins C, et al. SnapperDB: a database solution for routine sequencing analysis of bacterial isolates. Bioinformatics 2018; 34:3028-3029.
• Lagier JC, Bilen M, Cadoret F, Drancourt M, Fournier PE, La Scola B, Raoult D. Naming microorganisms: the contribution of the IHU Mediterranee Infection, Marseille, France. New Microbes New Infect 2018; 26:S89-S95.
• Chung M, Munro JB, Tettelin H, Dunning Hotopp JC. Using Core Genome Alignments To Assign Bacterial Species. mSystems 2018; 3:0.
• Chuvochina M, Rinke C, Parks DH, Rappe MS, Tyson GW, Yilmaz P, Whitman WB, Hugenholtz P. The importance of designating type material for uncultured taxa. Syst Appl Microbiol 2019; 42:15-21.
• Overmann J, Huang S, Nübel U, Hahnke RL, Tindall BJ. Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms. Systematic and Applied Microbiology 2019; 42:22-29.
• Paul B, Dixit G, Murali TS, Satyamoorthy K. Genome-based taxonomic classification. Genome 2019; 62:45-52.
• Ribot EM, Freeman M, Hise KB, Gerner-Smidt P. PulseNet: Entering the Age of Next-Generation Sequencing. Foodborne Pathog Dis 2019; 16:451-456.
• Rossello-Mora R, Whitman WB. Dialogue on the nomenclature and classification of prokaryotes. Syst Appl Microbiol 2019; 42:5-14.
• Stackebrandt E, Smith D. Paradigm shift in species description: the need to move towards a tabular format. Archives of Microbiology 2019; 201:143–145.
• Albuquerque L, Rainey FA. In memoriam - Milton Simoes da Costa (1948-2020). Int J Syst Evol Microbiol 2020; 70:2165-2166.
• Gajdács M. Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists. Acta Pharmaceutica Hungarica 2020; 89:99-108.
• Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 2020; 38:1079-1086.

2021-2025

• Dextro RB, Delbaje E, Cotta SR, Zehr JP, Fiore MF. Trends in Free-access Genomic Data Accelerate Advances in Cyanobacteria Taxonomy. J Phycol 2021; 57:1392-1402.
• Göker M. What can genome analysis offer for bacteria? In: Bridge P, Smith D, Stackebrandt E (eds), Trends in the systematics of bacteria and fungi, CAB International, Wallingford, 2021, pp. 255-281.
• Hugenholtz P, Chuvochina M, Oren A, Parks DH, Soo RM. Prokaryotic taxonomy and nomenclature in the age of big sequence data. ISME J 2021; 15:1879-1892.
• Liu C, Du MX, Abuduaini R, Yu HY, Li DH, Wang YJ, Zhou N, Jiang MZ, Niu PX, Han SS, et al. Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank. Microbiome 2021; 9:119.
• Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E, Knittel K, Amann R, Rossello-Mora R. Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 2021; 44:126218.
• On SLW. Current status and future perspectives of taxonomic subcommittees of the International Committee on Systematics of Prokaryotes (ICSP). Int J Syst Evol Microbiol 2021; 71:5046.
• Prakash O, Parmar M, Vaijanapurkar M, Rale V, Shouche YS. Recent trend, biases and limitations of cultivation-based diversity studies of microbes. FEMS Microbiology Letters 2021; 368:0.
• Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Davin AA, Waite DW, Whitman WB, Parks DH, Hugenholtz P. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol 2021; 6:946-959.
• Sanford RA, Lloyd KG, Konstantinidis KT, Loffler FE. Microbial Taxonomy Run Amok. Trends Microbiol 2021; 29:394-404.
• Caudill MT, Brayton KA. The Use and Limitations of the 16S rRNA Sequence for Species Classification of Anaplasma Samples. Microorganisms 2022; 10:605.
• Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S. A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Mol Biol Evol 2022; 39:msac135.
• Nouioui I, Sangal V. Advanced prokaryotic systematics: the modern face of an ancient science. New Microbes New Infect 2022; 49-50:101036.
• The Microbiology Society. Corrigendum: Correction to manuscripts describing the fatty acid composition of organisms submitted to IJSEM between 2014 and 2021. Int J Syst Evol Microbiol 2022; 72:5162.
• Rossello-Mora R, Konstantinidis KT, Amann R. How Systematic and Applied Microbiology will deal with two nomenclature codes (ICNP and SeqCode) for prokaryotes, and which classification standards are recommended for new taxa descriptions. Syst Appl Microbiol 2023; 46:126371.

Useful online tools concerning prokaryotic taxonomy:

• TYGS – Type (Strain) Genome Server
• BacDive – The Bacterial Diversity Metadatabase
• DSMZ Single-Gene Phylogenies and Gene Similarities Server
• Key to Peptidoglycan Types
• GGDC (Genome-To-Genome Distance Calculator) Web Server