M-pick, a modularity-based method for OTU picking of 16S rRNA sequences

BMC Bioinformatics. 2013 Feb 7;14:43. doi: 10.1186/1471-2105-14-43.

Abstract

Background: Binning 16S rRNA sequences into operational taxonomic units (OTUs) is an initial crucial step in analyzing large sequence datasets generated to determine microbial community compositions in various environments including that of the human gut. Various methods have been developed, but most suffer from either inaccuracies or from being unable to handle millions of sequences generated in current studies. Furthermore, existing binning methods usually require a priori decisions regarding binning parameters such as a distance level for defining an OTU.

Results: We present a novel modularity-based approach (M-pick) to address the aforementioned problems. The new method utilizes ideas from community detection in graphs, where sequences are viewed as vertices on a weighted graph, each pair of sequences is connected by an imaginary edge, and the similarity of a pair of sequences represents the weight of the edge. M-pick first generates a graph based on pairwise sequence distances and then applies a modularity-based community detection technique on the graph to generate OTUs to capture the community structures in sequence data. To compare the performance of M-pick with that of existing methods, specifically CROP and ESPRIT-Tree, sequence data from different hypervariable regions of 16S rRNA were used and binning results were compared.

Conclusions: A new modularity-based clustering method for OTU picking of 16S rRNA sequences is developed in this study. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance levels to define OTUs. The source code is available at http://plaza.ufl.edu/xywang/Mpick.htm.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Classification / methods
  • Cluster Analysis
  • Gastrointestinal Tract / microbiology
  • Genetic Variation
  • Humans
  • RNA, Ribosomal, 16S / genetics*
  • Sequence Analysis, DNA / methods*

Substances

  • RNA, Ribosomal, 16S