Konstantinidis Konstantinos T, Rosselló-Móra Ramon, Amann Rudolf
School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC-UIB), Esporles, Spain.
ISME J. 2017 Nov;11(11):2399-2406. doi: 10.1038/ismej.2017.113. Epub 2017 Jul 21.
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.
绝大多数微生物物种仍未得到培养，这严重限制了它们的分类学特征描述，进而限制了科学家之间的交流。尽管“暂定种（Candidatus）”被设计为对未培养分类单元进行分类的临时类别，但由于技术限制以及“暂定种”名称在官方命名法中缺乏优先权，它尚未被广泛接受。高通量测序为未培养微生物提供了丰富数据的分类学描述潜力，其质量可与培养生物的描述相媲美。为了充分实现这一潜力，需要有关如何进行这些描述的标准和指南。在这里，我们旨在概述这些标准，并绘制新的基于基因组的分类学路线图，该分类学至少在最初将与现有的分离株分类学并行但高度趋同。特别是，我们建议使用通过群体分箱或单细胞技术获得的DNA基因组序列作为以下方面的基础：（i）鉴定和系统发育定位，（ii）基于生物信息学的功能以及由此进行的表型预测，以及（iii）模式材料。我们还建议为未培养分类单元实施一个独立的命名系统，遵循与培养细菌和古菌相同的命名规则，但有自己的有效发表名称列表。如果被广泛采用，这个系统不仅将有助于全面描述“未培养的大多数”，还将提供一个统一的有效发表名称目录，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。
