Nature Communications (Jun 2021)

Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

  • Verónica Lloréns-Rico,
  • Sara Vieira-Silva,
  • Pedro J. Gonçalves,
  • Gwen Falony,
  • Jeroen Raes

DOI
https://doi.org/10.1038/s41467-021-23821-6
Journal volume & issue
Vol. 12, no. 1
pp. 1 – 12

Abstract

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Here, the authors use simulated quantitative gut microbial communities to benchmark the performance of 13 common data transformations in determining diversity as well as microbe-microbe and microbe-metadata associations, finding that quantitative approaches incorporating microbial load variation outperform computational strategies in downstream analyses, urging for a widespread adoption of quantitative approaches, or recommending specific computational transformations whenever determination of microbial load of samples is not feasible.