Practically delineating bacterial species with genealogical concordance

dc.contributor.authorVenter, S.N. (Stephanus Nicolaas)
dc.contributor.authorPalmer, Marike
dc.contributor.authorBeukes, Chrizelle Winsie
dc.contributor.authorChan, Wai Yin
dc.contributor.authorShin, Giyoon
dc.contributor.authorVan Zyl, Elritha
dc.contributor.authorSeale, Tarren
dc.contributor.authorCoutinho, Teresa A.
dc.contributor.authorSteenkamp, Emma Theodora
dc.contributor.emailfanus.venter@up.ac.zaen_ZA
dc.date.accessioned2017-10-10T05:39:15Z
dc.date.issued2017-10
dc.description.abstractBacterial species are commonly defined by applying a set of predetermined criteria, including DNA–DNA hybridization values, 16S rRNA gene sequence similarity, phenotypic data as well as genome-based criteria such as average nucleotide identity or digital DNA-DNA hybridization. These criteria mostly allow for the delimitation of taxa that resemble typical bacterial species. Their application is often complicated when the objective is to delineate new species that are characterized by significant population-level diversity or recent speciation. However, we believe that these complexities and limitations can be easily circumvented by recognizing that bacterial species represent unique and exclusive assemblages of diversity. Within such a framework, methods that account for the population processes involved in species evolution are used to infer species boundaries. A method such as genealogical concordance analysis is well suited to delineate a putative species. The existence of the new taxon is then interrogated using an array of traditional and genome-based characters. By making use of taxa in the genera Pantoea, Paraburkholderia and Escherichia we demonstrate in a step-wise process how genealogical concordance can be used to delimit a bacterial species. Genetic, phenotypic and biological criteria were used to provide independent lines of evidence for the existence of that taxon. Our six-step approach to species recognition is straightforward and applicable to bacterial species especially in the post-genomic era, with increased availability of whole genome sequences. In fact, our results indicated that a combined genome-based comparative and evolutionary approach would be the preferred alternative for delineating coherent bacterial taxa.en_ZA
dc.description.departmentForestry and Agricultural Biotechnology Institute (FABI)en_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.embargo2018-10-30
dc.description.librarianhj2017en_ZA
dc.description.sponsorshipThe South African National Research Foundation (NRF) and the Department of Science and Technology for funding through their Center of Excellence programme.en_ZA
dc.description.urihttp://link.springer.com/journal/10482en_ZA
dc.identifier.citationVenter, S.N., Palmer, M., Beukes, C.W. et al. Practically delineating bacterial species with genealogical concordance. Antonie van Leeuwenhoek (2017) 110: 1311-1325. https://doi.org/10.1007/s10482-017-0869-8.en_ZA
dc.identifier.issn0003-6072 (print)
dc.identifier.issn1572-9699 (online)
dc.identifier.other10.1007/s10482-017-0869-8
dc.identifier.urihttp://hdl.handle.net/2263/62619
dc.language.isoenen_ZA
dc.publisherSpringeren_ZA
dc.rights© Springer International Publishing Switzerland 2017. The original publication is available at : http://link.springer.comjournal/10482.en_ZA
dc.subjectBacterial taxonomyen_ZA
dc.subjectEscherichia colien_ZA
dc.subjectGenealogical concordanceen_ZA
dc.subjectParaburkholderiaen_ZA
dc.subjectPantoeaen_ZA
dc.subjectSpecies recognitionen_ZA
dc.subjectEpidemiologyen_ZA
dc.subjectIdentificationen_ZA
dc.subjectPolyphasic taxonomyen_ZA
dc.subjectHorizontal gene transfer (HGT)en_ZA
dc.subjectMultilocus sequence analysis (MLSA)en_ZA
dc.titlePractically delineating bacterial species with genealogical concordanceen_ZA
dc.typePostprint Articleen_ZA

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