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A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity | npj Biofilms and Microbiomes

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Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. Advertisement npj Biofilms and Microbiomes volume  2, Article number: 16004 (2016) Cite this article 50k Accesses 242 Citations 46 Altmetric Metrics details The standard pipeline for 16S amplicon analysis starts by clustering sequences within a percent sequence similarity threshold (typically 97%) into ‘Operational Taxonomic Units’ (OTUs). From each OTU, a single sequence is selected as a representative. This representative sequence is annotated, and that annotation is applied to all remaining sequences within that OTU. This perspective paper will discuss the known shortcomings of this standard approach using results obta

When we examined the OTUs that were generated using PSD, we found that many OTUs had a MSD or BLD that was >0.03 (see Figures 1 and 2). We found that 80.5% of the V3V5 OTUs had at least one sequence that was >3% dissimilar (MSD>0.03) from the representative sequence, and 2.7% of all sequences across all the V3V5 OTUs had a MSD >3% from the representative. In addition, 4.7% of the V3V5 OTUs were very diverse and had an average MSD>0.03. Figure 1 Box plots of the mean MSA and BLD across the different phyla for the V1V3 OTUs. We report the distribution of the mean MSA-based sequence…

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