Investigating microbial co-occurrence patterns based on metagenomic compositional data

Yuguang Ban, Lingling An, Hongmei Jiang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

58 Scopus citations


Motivation: The high-throughput sequencing technologies have provided a powerful tool to study the microbial organisms living in various environments. Characterizing microbial interactions can give us insights into how they live and work together as a community. Metagonomic data are usually summarized in a compositional fashion due to varying sampling/sequencing depths from one sample to another. We study the co-occurrence patterns of microbial organisms using their relative abundance information. Analyzing compositional data using conventional correlation methods has been shown prone to bias that leads to artifactual correlations. Results: We propose a novel method, regularized estimation of the basis covariance based on compositional data (REBACCA), to identify significant co-occurrence patterns by finding sparse solutions to a system with a deficient rank. To be specific, we construct the system using log ratios of count or proportion data and solve the system using the l1-norm shrinkage method. Our comprehensive simulation studies show that REBACCA (i) achieves higher accuracy in general than the existing methods when a sparse condition is satisfied; (ii) controls the false positives at a pre-specified level, while other methods fail in various cases and (iii) runs considerably faster than the existing comparable method. REBACCA is also applied to several real metagenomic datasets. Availability and implementation.

Original languageEnglish (US)
Pages (from-to)3322-3329
Number of pages8
Issue number20
StatePublished - Mar 25 2015

ASJC Scopus subject areas

  • Computational Mathematics
  • Molecular Biology
  • Biochemistry
  • Statistics and Probability
  • Computer Science Applications
  • Computational Theory and Mathematics


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