Distribution-based clustering: using ecology to refine the operational taxonomic unit

Applied and Environmental Microbiology
Sarah P PreheimEric J Alm

Abstract

16S rRNA sequencing, commonly used to survey microbial communities, begins by grouping individual reads into operational taxonomic units (OTUs). There are two major challenges in calling OTUs: identifying bacterial population boundaries and differentiating true diversity from sequencing errors. Current approaches to identifying taxonomic groups or eliminating sequencing errors rely on sequence data alone, but both of these activities could be informed by the distribution of sequences across samples. Here, we show that using the distribution of sequences across samples can help identify population boundaries even in noisy sequence data. The logic underlying our approach is that bacteria in different populations will often be highly correlated in their abundance across different samples. Conversely, 16S rRNA sequences derived from the same population, whether slightly different copies in the same organism, variation of the 16S rRNA gene within a population, or sequences generated randomly in error, will have the same underlying distribution across sampled environments. We present a simple OTU-calling algorithm (distribution-based clustering) that uses both genetic distance and the distribution of sequences across samples and demo...Continue Reading

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Related Concepts

Kinetic Polymerase Chain Reaction
Sequencing
Oligonucleotide Primers
Sequence Determinations, DNA
Organism
Microbial
Base Pairing
RNA, Ribosomal, 16S
Bacterial 16S RNA
Otus

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