Analysis of microbial compositions: a review of normalization and differential abundance analysis
Open accessAbstract
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.”
From Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma (2024) · cites this paper as [66]
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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)
- PMC
- PMC7710733
- 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
- gold
- doi.org
- 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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