Abstract
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.
Highlights
Recent advances in sequencing technology have enabled researchers to characterize microbial diversity at previously unattainable scales
One crucial step in such studies is the clustering of sequences into Operational Taxonomic Units (OTUs) of closely related organisms
This practice has repeatedly been called into question, arguing that the use of OTUs is not backed by microbial speciation theory
Summary
Recent advances in sequencing technology have enabled researchers to characterize microbial diversity at previously unattainable scales. The gold standard for microbial diversity units are theory-informed definitions that would comply with a commonly accepted concept of bacterial speciation; in other words, operational units of diversity should approximate ‘true’ bacterial taxa [2]. This implies two frequently cited criteria for theory-compliant diversity units: they should reflect phylogeny (by representing monophyletic groups of organisms) and ecology, since ecological differentiation has been postulated as an important driver of bacterial speciation [2,3,4,5,6,7,8]. While ecotype simulation has been valuable in characterizing the diversity of selected environments [13], it has been noted that recognized diversity clusters within several microbial clades can conflict with ecotype theory [11,14]
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