Updating the 97% identity threshold for 16S ribosomal RNA OTUs
Updating the 97% identity threshold for 16S ribosomal RNA OTUs
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DOI：
10.1093/bioinformatics/bty113
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发表时间：
2018-07-15
期刊：
影响因子：
5.8
通讯作者：
Edgar, Robert C.
中科院分区：
文献类型：
--
作者：
Edgar, Robert C.
动机：16S核糖体RNA（rRNA）基因被广泛用于调查微生物群落。序列通常被聚类为操作分类单位（OTU）作为物种的替代。典型的聚类阈值是97%的同一性，这是在1994年提出的几个16S rRNA序列可用，激励重新评估当前data.Results：使用一个大的高品质的16S rRNA序列从完成的基因组，我评估了对应的OTU的物种的五个代表性的聚类算法，使用四个精度指标。当调整到给定的度量标准时，所有算法都具有相当的准确性。全长序列的最佳同一性阈值与99%相似，V4高变区的最佳同一性阈值与100%相似。
Motivation: The 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Sequences are often clustered into Operational Taxonomic Units (OTUs) as proxies for species. The canonical clustering threshold is 97% identity, which was proposed in 1994 when few 16S rRNA sequences were available, motivating a reassessment on current data.Results: Using a large set of high-quality 16S rRNA sequences from finished genomes, I assessed the correspondence of OTUs to species for five representative clustering algorithms using four accuracy metrics. All algorithms had comparable accuracy when tuned to a given metric. Optimal identity thresholds were similar to 99% for full-length sequences and similar to 100% for the V4 hypervariable region.