Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

作者：Yan He, J. Gregory Caporaso, Xiaotao Jiang, Hua-Fang Sheng, Susan M. Huse, Jai Ram Rideout, R. C. Edgar, Evguenia Kopylova, William A. Walters, Rob Knight, Hongwei Zhou · 发表于：Microbiome · 年份：2015 · DOI：10.1186/s40168-015-0081-x · 被引用次数：185 · 研究领域：Microbial Community Ecology and Physiology、Gut microbiota and health、Genomics and Phylogenetic Studies

BACKGROUND: The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. RESULTS: Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. CONCLUSIONS: As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when ana...