Public human microbiome data are dominated by highly developed countries
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Abstract
The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack a full understanding of the global distribution of sampling in research studies. This information is crucial to better understand global patterns of microbiome-associated diseases and to extend the health benefits of this research to all populations. Here, we analyze the country of origin of all 444,829 human microbiome samples that are available from the world's 3 largest genomic data repositories, including the Sequence Read Archive (SRA). The samples are from 2,592 studies of 19 body sites, including 220,017 samples of the gut microbiome. We show that more than 71% of samples with a known origin come from Europe, the United States, and Canada, including 46.8% from the US alone, despite the country representing only 4.3% of the global population. We also find that central and southern Asia is the most underrepresented region: Countries such as India, Pakistan, and Bangladesh account for more than a quarter of the world population but make up only 1.8% of human microbiome samples. These results demonstrate a critical need to ensure more global representation of participants in microbiome studies.
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Microbiome members of individuals from non-westernized populations are underrepresented by current cultivation-based genomic catalogs, causing metagenomic profiling to miss large fractions of microbial diversity.
“Microbiome members of individuals from non-westernized populations are particularly underrepresented by current cultivation-based genomic catalogs causing metagenomic profiling approaches to miss large fractions of the microbial diversity in the samples.”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [36]
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- Authors
- Abdill, R. J., Adamowicz, E. M., & Blekhman, R.
- Affiliations
- University of Minnesota (US)
- Corresponding author
- Blekhman, Ran
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2022-02-15
- Volume
- 20
- Issue
- 2
- Pages
- e3001536
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC8846514
- OpenAlex
- W4213375238
- Cited by
- 221
- References
- 68
- Citations by year
- 2026: 51 · 2025: 58 · 2024: 47 · 2023: 46 · 2022: 18 · 2017: 1
- FWCI
- 14.37
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (R35GM128716)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Keywords
- human microbiome, sampling bias, geographical representation, gut microbiota, Sequence Read Archive, underrepresented groups, global health equity
- MeSH terms
- Gastrointestinal Microbiome, Asia, Bangladesh, Canada, Europe, Geography, Humans, India, Pakistan, United States, Developed Countries, Genomics, Metagenome, Metagenomics, Microbiota
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