Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.
Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.
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DOI：
10.1128/mbio.02136-14
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发表时间：
2014-11-18
期刊：
影响因子：
6.4
通讯作者：
Graf J
中科院分区：
文献类型：
--
作者：
Colston SM;Fullmer MS;Beka L;Lamy B;Gogarten JP;Graf J
生物分类学是微生物学的基础，因为它为生物的正确识别和命名提供了一个框架。细菌物种划分的“金标准”是由DNA-DNA杂交（DDH）确定的总体基因组相似性，DDH是一种技术上严格但有时可变的方法，可能会产生不一致的结果。下一代测序的改进导致细菌基因组序列和比较基因组数据的生物信息学工具的激增，例如平均核苷酸同一性（ANI），四核苷酸频率的相关性和基因组到基因组距离计算器，或计算机DDH（isDDH）。在这里，我们评估ANI和isDDH与系统发育研究相结合，使用气单胞菌属，一个分类学上具有挑战性的属，许多描述的物种和几个菌株，被重新分配到不同的物种作为测试案例。我们为33株气单胞菌菌株生成了改进的高质量基因组草图序列，并将其与23个公开的基因组相结合。ANI和isDDH的距离进行了测定，并从管家基因，核糖体蛋白质，和扩展的核心基因的多位点序列分析的同源性进行比较。扩展的核心系统发育分析表明，遥远的气单胞菌分支之间的关系是不一致的研究，使用较少的基因。ANI值≥96%和isDDH值≥70%一致地将来自相同种属菌株的基因组分组在一起。我们的研究证实了已知的错误鉴定，验证了最近的命名法修订，并揭示了一些基因组存放在GenBank中被错误命名。此外，还鉴定了两种可能代表新型气单胞菌属的菌株。DNA测序技术的改进使得能够产生大量高质量的基因组草图，并导致可获得的基因组数量急剧增加。这使得研究人员能够使用基因组数据来表征微生物。基于基因组序列的分类的优点包括可以容易地共享的数据和计算程序，促进分类方法的标准化，并通过在总体分析中提供更大的一致性来解决相互冲突的鉴定。使用气单胞菌作为测试案例，我们比较和验证不同的方法。根据我们的分析，我们建议的截止值的距离测量识别物种。准确的物种分类不仅对消除公共数据库中的错误，而且对确保对属内物种之间关系的推断的有效性以及临床和兽医诊断实验室的正确鉴定至关重要。
Prokaryotic taxonomy is the underpinning of microbiology, as it provides a framework for the proper identification and naming of organisms. The “gold standard” of bacterial species delineation is the overall genome similarity determined by DNA-DNA hybridization (DDH), a technically rigorous yet sometimes variable method that may produce inconsistent results. Improvements in next-generation sequencing have resulted in an upsurge of bacterial genome sequences and bioinformatic tools that compare genomic data, such as average nucleotide identity (ANI), correlation of tetranucleotide frequencies, and the genome-to-genome distance calculator, or in silico DDH (isDDH). Here, we evaluate ANI and isDDH in combination with phylogenetic studies using Aeromonas, a taxonomically challenging genus with many described species and several strains that were reassigned to different species as a test case. We generated improved, high-quality draft genome sequences for 33 Aeromonas strains and combined them with 23 publicly available genomes. ANI and isDDH distances were determined and compared to phylogenies from multilocus sequence analysis of housekeeping genes, ribosomal proteins, and expanded core genes. The expanded core phylogenetic analysis suggested relationships between distant Aeromonas clades that were inconsistent with studies using fewer genes. ANI values of ≥96% and isDDH values of ≥70% consistently grouped genomes originating from strains of the same species together. Our study confirmed known misidentifications, validated the recent revisions in the nomenclature, and revealed that a number of genomes deposited in GenBank are misnamed. In addition, two strains were identified that may represent novel Aeromonas species. Improvements in DNA sequencing technologies have resulted in the ability to generate large numbers of high-quality draft genomes and led to a dramatic increase in the number of publically available genomes. This has allowed researchers to characterize microorganisms using genome data. Advantages of genome sequence-based classification include data and computing programs that can be readily shared, facilitating the standardization of taxonomic methodology and resolving conflicting identifications by providing greater uniformity in an overall analysis. Using Aeromonas as a test case, we compared and validated different approaches. Based on our analyses, we recommend cutoff values for distance measures for identifying species. Accurate species classification is critical not only to obviate the perpetuation of errors in public databases but also to ensure the validity of inferences made on the relationships among species within a genus and proper identification in clinical and veterinary diagnostic laboratories.