LINgroups as a principled approach to compare and integrate multiple bacterial taxonomies
LINgroups as a principled approach to compare and integrate multiple bacterial taxonomies
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LINgroups 作为比较和整合多种细菌分类法的原则方法
DOI：
10.1145/3535508.3545546
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Heath, Lenwood S.
中科院分区：
文献类型：
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作者：
Mazloom, Reza;Pritchard, Leighton;Brown, C. Titus;Vinatzer, Boris A.;Heath, Lenwood S.
传统的分类学提供了一个从界到亚种的细菌和古菌的分类等级组织。最近，细菌分类学已经通过比较测序的基因组进行了更有力的量化，如在基因组分类数据库（GTDB）中，解析到属和种。这样的分类法在许多情况下都被证明是有用的，但缺乏更细粒度方法的灵活性和解决方案。我们应用我们的生命标识号（LIN）的方法作为一个共同的，定量的框架，将现有的（和未来的）细菌分类联系在一起，提高分辨率的基于基因组的分类群的歧视，并在物种水平以下的原则性的方式扩展分类识别。我们利用我们现有的LINgroup概念作为微生物的组织概念，这些微生物通过整体基因组相似性密切相关，以帮助解决由于基于基因组的重新分类而引起的微生物命名变化的一些混乱和不可预见的负面影响。我们从实验中获得的结果表明林斯和LIN组在分类之间的映射，不同的命名之间的翻译，并将它们整合到一个单一的分类框架的价值。
Traditional taxonomy provides a hierarchical organization of bacteria and archaea across taxonomic ranks from kingdom to subspecies. More recently, bacterial taxonomy has been more robustly quantified using comparisons of sequenced genomes, as in the Genome Taxonomy Database (GTDB), resolving down to genera and species. Such taxonomies have proven useful in many contexts, yet lack the flexibility and resolution of a more fine-grained approach. We apply our Life Identification Number (LIN) approach as a common, quantitative framework to tie existing (and future) bacterial taxonomies together, increase the resolution of genome-based discrimination of taxa, and extend taxonomic identification below the species level in a principled way. We utilize our existing concept of a LINgroup as an organizational concept for microorganisms that are closely related by overall genomic similarity, to help resolve some of the confusions and unforeseen negative effects of nomenclature changes of microbes due to genome-based reclassification. Our results obtained from experimentation demonstrate the value of LINs and LINgroups in mapping between taxonomies, translating between different nomenclatures, and integrating them into a single taxonomic framework.