Microbial taxonomy in the post-genomic era: Rebuilding from scratch?
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Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
KeywordsBacteria Archaea Microbes Taxonomy Genomics Evolution Open access
We thank CAPES, CNPq, FAPERJ, and NSF for funding. R.E. is supported by NSF Grants DEB-1046413 and CNS-1305112. M.F.P. acknowledges funding by NSF Grants DEB 0918333 and OCE 1441943, and the Gordon and Betty Moore Foundation. D.U is supported by internal funding from Oak Ridge National Labs, and from grants from the Office of Biological and Environmental Research in the DOE Office of Science.
- Forde BM, Ben Zakour NL, Stanton-Cook M et al (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One 9:e104400. doi: 10.1371/journal.pone.0104400 CrossRefPubMedCentralPubMedGoogle Scholar
- Konstantinidis KT, Stackebrandt E (2013) Defining taxonomic ranks. In: Rosenberg E, DeLong EF, Lory S, et al (eds) Prokaryotes (4th ed). Prokaryotic Biol. Symbiotic Assoc., 4th edn p 229Google Scholar
- Mayr E (1942) Systematics and the origin of species—from the viewpoint of a zoologist. Harvard Univ. Press, CambridgeGoogle Scholar
- Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P (2014) Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol 64:3821–3832. doi: 10.1099/ijs.0.063966-0
- Sneath PHA, Sokal RR (1973) The principles and practice of numerical classification. Numer. TaxonGoogle Scholar
- Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155Google Scholar
- Thompson FL, Thompson CC, Dias GM et al (2011b) The genus Listonella MacDonell and Colwell 1986 is a later heterotypic synonym of the genus Vibrio Pacini 1854 (Approved Lists 1980)—a taxonomic opinion. Int J Syst Evol Microbiol 61:3023–3027. doi: 10.1099/ijs.0.030015-0 CrossRefPubMedCentralPubMedGoogle Scholar
- Wayne LG, Brenner DJ, Colwell RR, et al (1987) International Committee on Systematic Bacteriology announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 463–464Google Scholar