Time to revisit polyphasic taxonomy

Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431–440. doi: 10.1038/Nrmicro1872

Amaral GRS, Dias GM, Wellington-Oguri M, Chimetto L, Campeão ME, Thompson FL, Thompson CC (2014) Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 64:357–365. doi: 10.1099/ijs.0.057927-0

Angus A, Agapakis CM, Fong S, Yerrapragada S, Estrada-de Los Santos P, Yang P, Song N, Kano S, Caballero-Mellado J, de Faria SM, Dakora FD, Weinstock G, Hirsch AM (2014) Plant-associated symbiotic Burkholderia species lack hallmark strategies required in mammalian pathogenesis. PLoS ONE. doi: 10.1371/journal.pone.0083779

Coenye T, Vandamme P (2003) Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ Microbiol 5:719–729. doi: 10.1046/j.1462-2920.2003.00471.x

Coenye T, Laevens S, Willems A, Ohlen M, Hannant W, Govan JRW, Gillis M, Falsen E, Vandamme P (2001) Burkholderia fungorum sp. nov., and Burkholderia caledonica sp. nov., two new species isolated from the environment, animals and human clinical samples. Int J Syst Evol Microbiol 51:1099–1107

Coenye T, Goris J, Spilker T, Lipuma JJ, Vandamme P (2002) Characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of Inquilinus limosus gen. nov. J Clin Microbiol 40:2062–2069. doi: 10.1128/JCM.40.6.2062

Colwell RR (1970) Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104:410–433

Compant S, Nowak J, Coenye T, Clément C, Ait Barka E, Clement C, Barka EA (2008) Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol Rev 32:607–626. doi: 10.1111/j.1574-6976.2008.00113.x

Deloger M, El Karoui M, Petit MA (2009) A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 191:91–99. doi: 10.1128/Jb.01202-08

Deris ZZ, Van Rostenberghe H, Habsah H, Noraida R, Tan GC, Chan YY, Rosliza AR, Ravichandran M (2010) First isolation of Burkholderia tropica from a neonatal patient successfully treated with imipenem. Int J Infect Dis 14:e73–e74. doi: 10.1016/j.ijid.2009.03.005

Desai AP, Stanley T, Atuan M, McKey J, Lipuma JJ, Rogers B, Jerris R (2012) Use of matrix assisted laser desorption ionisation-time of flight mass spectrometry in a paediatric clinical laboratory for identification of bacteria commonly isolated from cystic fibrosis patients. J Clin Pathol 65:835–838. doi: 10.1136/jclinpath-2012-200772

Estrada-de Los Santos P, Vinuesa P, Martínez-Aguilar L, Hirsch AM, Caballero-Mellado J (2013) Phylogenetic analysis of Burkholderia species by multilocus sequence analysis. Curr Microbiol 67:51–60. doi: 10.1007/s00284-013-0330-9

Gerrits G, Klaassen C, Coenye T, Vandamme P, Meis JF (2005) Burkholderia fungorum septicemia. Emerg Infect Dis 11:1115–1117

Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739. doi: 10.1038/Nrmicro1236

Gevers D, Dawyndt P, Vandamme P, Willems A, Vancanneyt M, Swings J, De Vos P (2006) Stepping stones towards a new prokaryotic taxonomy. Philos Trans R Soc B-Biological Sci 361:1911–1916. doi: 10.1098/Rstb.2006.1915

Goris J, De Vos P, Caballero-Mellado J, Park J, Falsen E, Quensen JF, Tiedje JM, Vandamme P (2004) Classification of the biphenyl and polychlorinated biphenyl-degrading strain LB400T and relatives as Burkholderia xenovorans sp. nov. Int J Syst Evol Microbiol 54:1677–1681. doi: 10.1099/ijs.0.63101-0

Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. doi: 10.1099/ijs.0.64483-0

Gyaneshwar P, Hirsch AM, Moulin L, Chen W-M, Elliott GN, Bontemps C, Estrada-de Los Santos P, Gross E, Dos Reis FB, Sprent JI, Young JPW, James EK (2011) Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. Mol plantmicrobe Interact MPMI 24:1276–1288. doi: 10.1094/MPMI-06-11-0172

Hibbett DS, Taylor JW (2013) Fungal systematics: is a new age of enlightenment at hand? Nat Rev Microbiol 11:129–133. doi: 10.1038/nrmicro2963

Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595. doi: 10.1186/1471-2105-11-595

Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572. doi: 10.1073/pnas.0409727102

Lemaire B, Robbrecht E, Wyk B, Oevelen S, Verstraete B, Prinsen E, Smets E, Dessein S (2011) Identification, origin, and evolution of leaf nodulating symbionts of Sericanthe (Rubiaceae). J Microbiol 6:935–941. doi: 10.1007/s12275-011-1163-5

Lemaire B, Van Oevelen S, De Block P, Verstraete B, Smets E, Prinsen E, Dessein S (2012) Identification of the bacterial endosymbionts in leaf nodules of Pavetta (Rubiaceae). Int J Syst Evol Microbiol 62:202–209. doi: 10.1099/ijs.0.028019-0

Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou JJ, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145. doi: 10.1073/pnas.95.6.3140

Oren A, Garrity GM (2014) Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie Van Leeuwenhoek. doi: 10.1007/s10482-013-0084-1

Parke JL, Gurian-Sherman D (2001) Diversity of the Burkholderia cepacia complex and implications for risk assessment of biological control strains. Annu Rev Phytopathol 39:225–258. doi: 10.1146/annurev.phyto.39.1.225

Peeters C, Zlosnik JEA, Spilker T, Hird TJ, Lipuma JJ, Vandamme P (2013) Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere. Syst Appl Microbiol 36:483–489. doi: 10.1016/j.syapm.2013.06.003

Ramasamy D, Mishra AK, Lagier J-C, Padhmanabhan R, Rossi M, Sentausa E, Raoult D, Fournier P-E (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391. doi: 10.1099/ijs.0.057091-0

Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. doi: 10.1073/pnas.0906412106

Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690

Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonça-Previato L, James EK, Venturi V (2012) Common features of environmental and potentially beneficial plant-associated Burkholderia. Microb Ecol 63:249–266. doi: 10.1007/s00248-011-9929-1

Sutcliffe IC, Trujillo ME, Goodfellow M (2012) A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie Van Leeuwenhoek 101:13–20. doi: 10.1007/s10482-011-9664-0

Sutcliffe IC, Trujillo ME, Whitman WB, Goodfellow M (2013) A call to action for the international committee on systematics of prokaryotes. Trends Microbiol 21:51–52. doi: 10.1016/j.tim.2012.11.004

Tamames J, Rosselló-Móra R (2012) On the fitness of microbial taxonomy. Trends Microbiol 20:514–516. doi: 10.1016/j.tim.2012.08.012

Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266. doi: 10.1099/Ijs.0.016949-0

Van Oevelen S, De Wachter R, Vandamme P, Robbrecht E, Prinsen E (2004) “Candidatus Burkholderia calva” and “Candidatus Burkholderia nigropunctata” as leaf gall endosymbionts of African Psychotria. Int J Syst Evol Microbiol 54:2237–2239. doi: 10.1099/ijs.0.63188-0

Vandamme P, Pot B, Gillis M, DeVos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

Vandamme P, Holmes B, Vancanneyt M, Coenye T, Hoste B, Coopman R, Revets H, Lauwers S, Gillis M, Kersters K, Govan JRW (1997) Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov. Int J Syst Bacteriol 47:1188–1200

Vanlaere E, Baldwin A, Gevers D, Henry D, De Brandt E, LiPuma JJ, Mahenthiralingam E, Speert DP, Dowson C, Vandamme P (2009) Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol 59:102–111. doi: 10.1099/Ijs.0.001123-0

Verstraete B, Van Elst D, Steyn H, Van Wyk B, Lemaire B, Smets E, Dessein S (2011) Endophytic bacteria in toxic South African plants: identification, phylogeny and possible involvement in gousiekte. PLoS ONE. doi: 10.1371/annotation/e7fa3cdf-c7bc-439f-83a2-36da63ef6c08

Verstraete B, Peeters C, van Wyk B, Smets E, Dessein S, Vandamme P (2014) Intraspecific variation in Burkholderia caledonica: Europe vs. Africa and soil vs. endophytic isolates. Syst Appl Microbiol in press: 1–6. doi: 10.1016/j.syapm.2013.12.001

Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T, Arakawa M (1992) Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 36:1251–1275