Bach Evelise, Volpiano Camila Gazolla, Sant'Anna Fernando Hayashi, Passaglia Luciane Maria Pereira
Instituto de Biociências, Departamento de Genética and Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.
Hospital Moinhos de Vento, Programa de Apoio ao Desenvolvimento Institucional do Sistema Único de Saúde (PROADI - SUS), Porto Alegre, RS, Brazil.
Genet Mol Biol. 2023 Nov 3;46(3 Suppl 1):e20230122. doi: 10.1590/1678-4685-GMB-2023-0122. eCollection 2023.
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.
已使用基于基因组的工具重新审视了伯克霍尔德菌复合群（sensu lato，s.l.）的分类学，这些工具有助于区分亲缘关系密切的物种。该类群中的许多物种通过表型特征和16S rRNA基因序列分析无法区分。此外，它们在物种界定的模糊区域（95 - 96%）也表现出全基因组平均核苷酸同一性（ANI）值，这可能会影响其正确分类。在这项工作中，我们提供了一个更新的伯克霍尔德菌复合群分类学，重点关注亲缘关系密切的物种，并为那些开展基于基因组的分类学研究的人员提供了其他建议。我们表明，分别应用95%和70%的通用临界值的ANI和数字DNA - DNA杂交（dDDH）相结合，能够成功区分伯克霍尔德菌复合群的物种。使用具有这种实用标准的基因组指标，我们证明了：i）岛屿副伯克霍尔德菌（Paraburkholderia insulsa）应被视为真菌副伯克霍尔德菌（Paraburkholderia fungorum）的晚出异名；ii）斯泰因副伯克霍尔德菌（Paraburkholderia steynii）因含有共生基因而与土壤副伯克霍尔德菌（P. terrae）不同；iii）一些副伯克霍尔德菌尽管共享接近95%的ANI值，但基于dDDH值确实是不同的物种；iv）从基因组角度来看，一些伯克霍尔德菌复合群确实代表新物种；iv）由于质量问题，一些基因组序列应谨慎评估。
