Hypothesis testing and power calculations for taxonomic-based human microbiome data

PLoS One. 2012;7(12):e52078. doi: 10.1371/journal.pone.0052078. Epub 2012 Dec 20.


This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of hypothesis and power/sample size calculations, and applies them for illustration to taxonomic abundance distribution and rank abundance distribution data using HMP Jumpstart data on 24 subjects for saliva, subgingival, and supragingival samples. Software for running these analyses is available.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adolescent
  • Adult
  • Algorithms
  • Bacteria / classification
  • Bacteria / genetics
  • Biodiversity
  • Computational Biology
  • Female
  • Gingiva / microbiology
  • Humans
  • Male
  • Metagenome*
  • Models, Statistical*
  • Reproducibility of Results
  • Young Adult