Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale.操作分类单元（Operational Taxonomic Units, OTUs）通常被定义为相似16S/18S核糖体RNA（rRNA）序列的聚类簇，是大规模微生物群落特征分析中应用最广泛的基础多样性单元。然而，目前仍不明确各类已提出的OTU聚类算法能在多大程度上近似“真实”的微生物类群。本研究基于如下假设展开探究：与真实微生物类群一致，OTU应表现出可测量的生境偏好（生态位保守性），以此分析OTU的生态一致性。我们对现有微生物序列数据开展全球范围的全面调研，系统解析序列注释信息以获取采样位点的宽泛生态描述。基于这些数据，我们发现基于序列的微生物OTU普遍呈现出较高水平的生态一致性，但不同OTU聚类方法所得到的该信号强度存在显著差异。若假设生态一致性可作为聚类质量的客观外部基准，则本研究认为层级完全连锁聚类能生成最具生态一致性的分区结果，应作为OTU聚类的默认选择。据我们所知，这是首次在全球尺度上，以外部的、具有生物学意义的参数作为基准来评估聚类质量的研究。