Journal
NATURE COMMUNICATIONS
Volume 13, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-021-27917-x
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Funding
- Stanford Center for Innovation in Global Health
- NIH [P30 CA124435]
- Genetics Bioinformatics Service Center
- Sloan Foundation Fellowship
- National Institute of Allergy and Infectious Diseases [R01AI148623]
- ational Science Foundation Graduate Research Fellowship
- Stanford Computational, Evolutionary, and Human Genetics Pre-Doctoral Fellowship
- Stanford Graduate Fellowships in Science and Engineering program
- Fogarty Global Health Equity Scholar award [TW009338]
- Fogarty International Centre, National Institutes of Health [K43TW010698]
- South African National Research Foundation [CPRR160421162721]
- African Partnership for Disease Control
- National Human Genome Research Institute as part of the H3A Consortium [U54HG006938]
- Department of Science and Innovation
- University of the Witwatersrand
- Medical Research Council, South Africa
- Wellcome Trust, UK [058893/Z/99/A, 069683/Z/02/Z, 085477/Z/08/Z, 085477/B/08/Z]
- INDEPTH consortium
- Stanford Research Computing Center
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In this study, researchers analyzed the gut microbiome of individuals living in rural and urban areas of South Africa using short- and long-read DNA sequencing. They found transitional composition, high inter-individual diversity, and many undescribed taxa. This study highlights the importance of understanding the gut microbiota in different populations for a comprehensive understanding of health and disease.
In this study, Wits and Stanford researchers use short- and long-read DNA sequencing to profile the gut microbiome of women living in rural and urban South Africa and identify transitional composition, high inter-individual diversity, and many undescribed taxa. Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple western-nonwestern axis and contains undescribed microbial diversity.
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