Faculty of Computer Science, Dalhousie University, 6050 University Avenue, PO Box 15000, Halifax, Nova Scotia B3H 4R2, Canada.
Trends Microbiol. 2015 Nov;23(11):671-679. doi: 10.1016/j.tim.2015.08.009. Epub 2015 Oct 1.
The names and lineages of microorganisms are critical to our understanding of the microbiome. However, microbial taxonomy and phylogeny are in perpetual flux, with emerging criteria being used to rename and reshape our views of the microbial world. Different candidate molecular and nonmolecular criteria are often broadly consistent with one another, which underpins the pluralistic approach to taxonomy. However, the taxonomic picture is clouded when underlying criteria are not in agreement, or when reference datasets contain erroneously named organisms. How does the shifting taxonomic landscape impact our interpretation of microbial communities, especially in the face of inconsistencies and errors? How can taxonomy be applied in a consistent way when different users have different requirements of the classifications that emerge? The key path forward involves finding ways to integrate conflicting taxonomic criteria, choosing the right units of analysis for microbiomic studies, and making molecular taxonomy transparent and accessible in a way that complements current genomic resources.
微生物的名称和谱系对于我们理解微生物组至关重要。然而，微生物分类学和系统发生学处于不断变化之中，新出现的标准被用来重新命名和重塑我们对微生物世界的看法。不同的候选分子和非分子标准通常彼此之间广泛一致，这为分类学的多元方法提供了基础。然而，当基础标准不一致时，或者参考数据集包含错误命名的生物体时，分类学图景就会变得模糊。不断变化的分类学景观如何影响我们对微生物群落的解释，特别是在面对不一致和错误时？当不同的用户对出现的分类有不同的要求时，如何以一致的方式应用分类学？前进的关键途径包括寻找方法来整合冲突的分类标准，为微生物组研究选择合适的分析单位，并以一种补充现有基因组资源的方式使分子分类学透明和易于访问。
