Differential abundance analysis for microbial marker-gene surveys

Joseph N. Paulson, O. Colin Stine, Héctor Corrada Bravo, Mihai Pop

Research output: Contribution to journalArticlepeer-review

850 Scopus citations


We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling - a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.

Original languageEnglish (US)
Pages (from-to)1200-1202
Number of pages3
JournalNature Methods
Issue number12
StatePublished - Dec 2013
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology


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