Uncultivated microbes in need of their own taxonomy
Uncultivated microbes in need of their own taxonomy
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DOI：
10.1038/ismej.2017.113
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发表时间：
2017-11-01
期刊：
影响因子：
11
通讯作者：
Amann, Rudolf
中科院分区：
文献类型：
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作者：
Konstantinidis, Konstantinos T.;Rossello-Mora, Ramon;Amann, Rudolf
绝大多数微生物物种仍未被培养，这严重限制了它们的分类特征，从而限制了科学家之间的交流。虽然Candidatus是作为一种临时分类来分类未培养的分类群，但由于技术限制和Candidatus名称在官方命名法中缺乏优先级，它尚未被广泛接受。高通量测序为未培养微生物的分类描述提供了数据丰富的潜力，其质量可与培养生物的分类描述相媲美。为了充分实现这一潜力，需要关于如何执行这些描述的标准和指导方针。在这里，我们的目标是概述这些标准，并为新的基于基因组的分类绘制路线图，至少在最初，将与现有的分离株分类平行，但高度收敛。特别是，我们建议使用DNA基因组序列，通过群体分类或单细胞技术恢复，作为(i)鉴定和系统发育定位的基础，（ii）基于生物信息学的功能和表型预测的基础，以及（iii）类型材料。我们还建议对未培养的分类群实施独立的命名系统，遵循与培养细菌和古细菌相同的命名规则，但有自己的有效公布名称列表。如果被广泛采用，这一系统不仅有助于全面描述“未受过教育的大多数人”，而且还提供了一个统一的有效出版名称目录，从而避免同义词和混淆。我们还建议成立一个由国际微生物学会支持的专家委员会来管理新的分类系统。
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms. In order to fully realize this potential, standards and guidelines on how to perform these descriptions are needed. Here we aimed to outline these standards and draw the roadmap for a new genome-based taxonomy that, at least initially, would be parallel but highly convergent to the one in existence for isolates. In particular, we recommend the use of DNA genome sequences, recovered by population binning or single-cell techniques, as the basis for (i) identification and phylogenetic placement, (ii) bioinformatics-based functional and thus phenotypic predictions, as well as (iii) type material. We also recommend the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured Bacteria and Archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the 'uncultivated majority', but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion. We also suggest that a committee of experts, supported by an international microbiological society, should be formed to govern the new classification system.