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Brewster R, Tamburini FB, Asiimwe E, Oduaran O, Hazelhurst S, Bhatt AS. Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation. Trends Microbiol 2019; 27:824-835. [PMID: 31178123 DOI: 10.1016/j.tim.2019.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/09/2019] [Accepted: 05/15/2019] [Indexed: 12/16/2022]
Abstract
Descriptive and translational investigations into the human gut microbiome (GM) are rapidly expanding; however, studies are largely restricted to industrialized populations in the USA and Europe. Little is known about microbial variability and its implications for health and disease in other parts of the world. Populations in Africa are particularly underrepresented. What limited research has been performed has focused on a few subject domains, including the impact of long-term lifestyle and dietary factors on GM ecology, its maturation during infancy, and the interrelationships between the microbiome, infectious disease, and undernutrition. Recently, international consortia have laid the groundwork for large-scale genomics and microbiome studies on the continent, with a particular interest in the epidemiologic transition to noncommunicable disease. Here, we survey the current landscape of GM scholarship in Africa and propose actionable recommendations to improve research capacity and output.
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Affiliation(s)
- Ryan Brewster
- School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Edgar Asiimwe
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Ovokeraye Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa; School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ami S Bhatt
- School of Medicine, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine (Hematology), Stanford University, Stanford, CA, USA.
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Jha AR, Davenport ER, Gautam Y, Bhandari D, Tandukar S, Ng KM, Fragiadakis GK, Holmes S, Gautam GP, Leach J, Sherchand JB, Bustamante CD, Sonnenburg JL. Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol 2018; 16:e2005396. [PMID: 30439937 PMCID: PMC6237292 DOI: 10.1371/journal.pbio.2005396] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 10/15/2018] [Indexed: 01/04/2023] Open
Abstract
The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to separate the contributions of human genetic and geographic factors from lifestyle. Whether shifts away from the foraging lifestyle that characterize much of humanity's past influence the gut microbiome, and to what degree, remains unclear. Here, we characterize the stool bacterial composition of four Himalayan populations to investigate how the gut community changes in response to shifts in traditional human lifestyles. These groups led seminomadic hunting-gathering lifestyles until transitioning to varying levels of agricultural dependence upon farming. The Tharu began farming 250-300 years ago, the Raute and Raji transitioned 30-40 years ago, and the Chepang retain many aspects of a foraging lifestyle. We assess the contributions of dietary and environmental factors on their gut-associated microbes and find that differences in the lifestyles of Himalayan foragers and farmers are strongly correlated with microbial community variation. Furthermore, the gut microbiomes of all four traditional Himalayan populations are distinct from that of the Americans, indicating that industrialization may further exacerbate differences in the gut community. The Chepang foragers harbor an elevated abundance of taxa associated with foragers around the world. Conversely, the gut microbiomes of the populations that have transitioned to farming are more similar to those of Americans, with agricultural dependence and several associated lifestyle and environmental factors correlating with the extent of microbiome divergence from the foraging population. The gut microbiomes of Raute and Raji reveal an intermediate state between the Chepang and Tharu, indicating that divergence from a stereotypical foraging microbiome can occur within a single generation. Our results also show that environmental factors such as drinking water source and solid cooking fuel are significantly associated with the gut microbiome. Despite the pronounced differences in gut bacterial composition across populations, we found little differences in alpha diversity across lifestyles. These findings in genetically similar populations living in the same geographical region establish the key role of lifestyle in determining human gut microbiome composition and point to the next challenging steps of determining how large-scale gut microbiome reconfiguration impacts human biology.
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Affiliation(s)
- Aashish R. Jha
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Center for Computational, Evolutionary, and Human Genetics, Stanford University, Stanford, California, United States of America
| | - Emily R. Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yoshina Gautam
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Dinesh Bhandari
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
| | - Katharine M. Ng
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Gabriela K. Fragiadakis
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | | | - Jeff Leach
- Human Food Project, Terlingua, Texas, United States of America
- Department of Twin Research and Genetic Epidemiology, King’s College London, St. Thomas’ Hospital, London, United Kingdom
| | | | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Center for Computational, Evolutionary, and Human Genetics, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- Center for Human Microbiome Studies, Stanford University, Stanford, California, United States of America
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