Defining bacterial species in the genomic era: insights from the genus Acinetobacter.
Defining bacterial species in the genomic era: insights from the genus Acinetobacter.
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DOI：
10.1186/1471-2180-12-302
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发表时间：
2012-12-23
期刊：
影响因子：
4.2
通讯作者：
Pallen MJ
中科院分区：
文献类型：
--
作者：
Chan JZ;Halachev MR;Loman NJ;Constantinidou C;Pallen MJ
微生物分类学仍然是一门保守的学科，依赖于从纯培养和技术中生长获得的表型信息，这些技术既耗时又难以标准化，特别是与现代高通量基因组测序的简便性相比。在这里，利用不动杆菌属作为测试案例，我们检查细菌分类学是否可以放弃表型方法和DNA-DNA杂交，而完全依赖于基因组序列数据的分析。为了实现这一目标，我们生成了一组13个新的基因组草稿序列，代表10个物种，将它们与其他公开可用的基因组序列相结合，并对这38株属于该属的菌株进行了分析。我们发现，基于16S rRNA基因序列的分析不能描述被接受的物种。然而，核心基因组系统发育树证明与目前接受的该属分类一致，同时也确定了集合或数据库中的三个菌株错误分类。在基于距离的快速方法中，我们发现平均核苷酸同一性(ANI)分析提供了与传统和系统发育分类一致的结果，而基于基因含量的方法似乎受到水平基因转移的影响太大，与以前接受的物种不一致。我们认为，核心基因组系统发育分析和ANI的结合为细菌物种的划分提供了一种合适的方法，即细菌物种被定义为具有至少95%成对ANI的基因组的单系群。建议的方法是向后兼容的；它提供了一种可扩展和统一的方法，既适用于可培养物种，也适用于非可培养物种；比传统分类学方法更快、更便宜；很容易在研究机构之间复制和转移；最后，符合达尔文的分类尽可能成为系谱的愿景。
Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical.
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影响因子：
3.2
作者：
Godreuil, Sylvain;Cohan, Frederick;Tibayrenc, Michel
通讯作者：
Tibayrenc, Michel
DOI：
10.1099/00207713-47-4-1179
发表时间：
1997-10-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
Janssen, P;Maquelin, K;Dijkshoorn, L
通讯作者：
Dijkshoorn, L
DOI：
10.1099/00207713-42-1-166
发表时间：
1992-01-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
FOX, GE;WISOTZKEY, JD;JURTSHUK, P
通讯作者：
JURTSHUK, P
影响因子：
9.4
作者：
GERNERSMIDT, P;TJERNBERG, I;URSING, J
通讯作者：
URSING, J
影响因子：
5.1
作者：
Heuer, Holger;Kopmann, Christoph;Smalla, Kornelia
通讯作者：
Smalla, Kornelia