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.
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