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Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species
The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Sociedade Brasileira de Genética
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629849/ https://www.ncbi.nlm.nih.gov/pubmed/37935243 http://dx.doi.org/10.1590/1678-4685-GMB-2023-0122 |
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author | Bach, Evelise Volpiano, Camila Gazolla Sant’Anna, Fernando Hayashi Passaglia, Luciane Maria Pereira |
author_facet | Bach, Evelise Volpiano, Camila Gazolla Sant’Anna, Fernando Hayashi Passaglia, Luciane Maria Pereira |
author_sort | Bach, Evelise |
collection | PubMed |
description | The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns. |
format | Online Article Text |
id | pubmed-10629849 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Sociedade Brasileira de Genética |
record_format | MEDLINE/PubMed |
spelling | pubmed-106298492023-11-08 Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species Bach, Evelise Volpiano, Camila Gazolla Sant’Anna, Fernando Hayashi Passaglia, Luciane Maria Pereira Genet Mol Biol 60 years of the PPGBM UFRGS - Special Issue The taxonomy of Burkholderia sensu lato (s.l.) has been revisited using genome-based tools, which have helped differentiate closely related species. Many species from this group are indistinguishable through phenotypic traits and 16S rRNA gene sequence analysis. Furthermore, they also exhibit whole-genome Average Nucleotide Identity (ANI) values in the twilight zone for species circumscription (95-96%), which may impair their correct classification. In this work, we provided an updated Burkholderia s.l. taxonomy focusing on closely related species and give other recommendations for those developing genome-based taxonomy studies. We showed that a combination of ANI and digital DNA-DNA hybridization (dDDH) applying the universal cutoff values of 95% and 70%, respectively, successfully discriminates Burkholderia s.l. species. Using genome metrics with this pragmatic criterion, we demonstrated that i) Paraburkholderia insulsa should be considered a later heterotypic synonym of Paraburkholderia fungorum; ii) Paraburkholderia steynii differs from P. terrae by harboring symbiotic genes; iii) some Paraburkholderia are indeed different species based on dDDH values, albeit sharing ANI values close to 95%; iv) some Burkholderia s.l. indeed represent new species from the genomic viewpoint; iv) some genome sequences should be evaluated with care due to quality concerns. Sociedade Brasileira de Genética 2023-11-03 /pmc/articles/PMC10629849/ /pubmed/37935243 http://dx.doi.org/10.1590/1678-4685-GMB-2023-0122 Text en https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License |
spellingShingle | 60 years of the PPGBM UFRGS - Special Issue Bach, Evelise Volpiano, Camila Gazolla Sant’Anna, Fernando Hayashi Passaglia, Luciane Maria Pereira Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species |
title | Genome-based taxonomy of Burkholderia sensu lato:
Distinguishing closely related species |
title_full | Genome-based taxonomy of Burkholderia sensu lato:
Distinguishing closely related species |
title_fullStr | Genome-based taxonomy of Burkholderia sensu lato:
Distinguishing closely related species |
title_full_unstemmed | Genome-based taxonomy of Burkholderia sensu lato:
Distinguishing closely related species |
title_short | Genome-based taxonomy of Burkholderia sensu lato:
Distinguishing closely related species |
title_sort | genome-based taxonomy of burkholderia sensu lato:
distinguishing closely related species |
topic | 60 years of the PPGBM UFRGS - Special Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10629849/ https://www.ncbi.nlm.nih.gov/pubmed/37935243 http://dx.doi.org/10.1590/1678-4685-GMB-2023-0122 |
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