Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence
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Abstract
The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.
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Bacteroides has been used to distinguish between developing (low Bacteroides abundance) and industrialized (high Bacteroides abundance) populations.
“Bacteroides has been used to distinguish between developing (low Bacteroides abundance) and industrialized (high Bacteroides abundance) populations [22–28, 30]”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [30]
Treponema within family Spirochetaceae is a common constituent of hunter-gatherer gut microbiomes and a catabolizer of fibrous plant materials (cellulose and xylans) that form a large component of Hadza diets.
“in particular, the genus Treponema within family Spirochetaceae, which is a common constituent of hunter-gatherer gut microbiomes [24–27, 30] and a catabolizer of fibrous plant materials (cellulose and xylans) that form a large component of Hadza diets [24]”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [30]
The Hadza have the highest abundance of Prevotellaceae and Spirochetaceae among populations in this cohort.
“they have the highest abundance of Prevotellaceae and Spirochetaceae [24–27, 30]”
From Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana (2019) · cites this paper as [30]
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Response of the human gut and saliva microbiome to urbanization in Cameroon
Lokmer, A., Aflalo, S., Amougou, N., Lafosse, S., Froment, A., Tabe, F. E., Poyet, M., Groussin, M., Said-Mohamed, R., & Ségurel, L. (2020) · Scientific Reports · doi:10.1038/s41598-020-59849-9 · Cited by 46 · see citing works
Self-citationThe shrinking human gut microbiome
Moeller, A. H. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.04.002 · Cited by 50 · see citing works
- Authors
- Morton, E. R., Lynch, J., Froment, A., Lafosse, S., Heyer, E., Przeworski, M., Blekhman, R., & Ségurel, L.
- Affiliations
- University of Minnesota (US)
- Centre National de la Recherche Scientifique (FR)
- Columbia University (US)
- Corresponding author
- Morton, Elise R.
- Blekhman, Ran
- Ségurel, Laure
- Venue
- PLOS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-11-30
- Volume
- 11
- Issue
- 11
- Pages
- e1005658
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC4664238
- OpenAlex
- W2182173958
- Cited by
- 231
- References
- 80
- Citations by year
- 2026: 14 · 2025: 12 · 2024: 30 · 2023: 22 · 2022: 16 · 2021: 26 · 2020: 21 · 2019: 31 · 2018: 23 · 2017: 26 · 2016: 8 · 2015: 2
- FWCI
- 8.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Howard Hughes Medical Institute
- Agence Nationale de la Recherche (ANR-11-BSV7-0011)
- CHIST-ERA
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Medicine › Infectious Diseases › Amoebic Infections and Treatments
- Keywords
- gut microbiota, Entamoeba, subsistence modes, hunter-gatherers, Bantu peoples, Pygmies, intestinal parasites, microbiome diversity, autoimmune disease, genetic ancestry, industrialization
- MeSH terms
- Gastrointestinal Microbiome, Animals, Diet, Entamoeba, Feces, Fishes, Humans, Phenotype, Rural Population, Tanzania, Genetic Variation, Black People
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