Establishing microbial composition measurement standards with reference frames

Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number of microorganisms, to accurately determine taxonomic shifts. Therefore, most studies rely on relative abundance data. Here, we demonstrate common pitfalls in comparing relative abundance across samples and identify two solutions that reveal microbial changes without the need to estimate total microbial load. We define the notion of "reference frames", which provide deep intuition about the compositional nature of microbiome data. In an oral time series experiment, reference frames alleviate false positives and produce consistent…

• NS
  National Science Foundation

  Awards: GRFP DGE-1144086, 1144086, DBI-1565057, DGE-1144086
• AP
  Alfred P. Sloan Foundation

  Award: G-2017-9838
• UO
  University of California, San Diego
• NI
  National Institute of Dental and Craniofacial Research

  Award: 1F31DE028478
• JP
  Janssen Pharmaceuticals

  Award: 20175015