Cited by 345Gut microbiota and healthMicrobial Community Ecology and PhysiologyGenomics and Phylogenetic Studies

Analysis of microbial compositions: a review of normalization and differential abundance analysis

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Lin, Huang, Peddada, Shyamal Das·2020·npj Biofilms and Microbiomes

Abstract

Increasingly, researchers are discovering associations between microbiome and a wide range of human diseases such as obesity, inflammatory bowel diseases, HIV, and so on. The first step towards microbiome wide association studies is the characterization of the composition of human microbiome under different conditions. Determination of differentially abundant microbes between two or more environments, known as differential abundance (DA) analysis, is a challenging and an important problem that has received considerable interest during the past decade. It is well documented in the literature that the observed microbiome data (OTU/SV table) are relative abundances with an excess of zeros. Since relative abundances sum to a constant, these data are necessarily compositional. In this article we review some recent methods for DA analysis and describe their strengths and weaknesses.

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  • Differential ranking is robust to the choice of the alr reference feature, and ranks produced from relative abundances are identical to the ranks of absolute abundances.

    “A recent approach called differential ranking is robust to the choice of the alr reference feature, and ranks produced from relative abundances are identical to the ranks of absolute abundances66,67.”

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  1. [46]Chen, Y., McCarthy, D., Robinson, M. & Smyth, G. K. edger: differential expression analysis of digital gene expression data user’s guide. http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf (2014). PMC2796818 19910308

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Authors
Lin, H., & Peddada, S. D.
Affiliations
National Institutes of Health (US)
Corresponding author
Peddada, Shyamal Das
Venue
npj Biofilms and Microbiomes
Published
2020-12-02
Volume
6
Issue
1
Pages
60-60
ISSN
2055-5008 (ISSN-L)
OpenAlex
W3109541743
Cited by
341
References
68
Citations by year
2026: 57 · 2025: 73 · 2024: 67 · 2023: 77 · 2022: 55 · 2021: 11
FWCI
3.45
Type
journal article
Language
en
Open access
Locations
  • npj Biofilms and Microbiomes (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
University of Pittsburgh
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
microbiome, differential abundance, compositional data, normalization, zero-inflated data, OTU table, sequencing read counts, human microbiome
MeSH terms
Gastrointestinal Microbiome, Bacteria, Humans, Models, Theoretical, Mouth, Phylogeny

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