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Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa

Author

Listed:
  • Fiona B. Tamburini

    (Stanford University)

  • Dylan Maghini

    (Stanford University)

  • Ovokeraye H. Oduaran

    (University of the Witwatersrand)

  • Ryan Brewster

    (Stanford University)

  • Michaella R. Hulley

    (University of the Witwatersrand
    National Health Laboratory Service & University of the Witwatersrand)

  • Venesa Sahibdeen

    (National Health Laboratory Service & University of the Witwatersrand)

  • Shane A. Norris

    (University of the Witwatersrand
    University of Southampton)

  • Stephen Tollman

    (University of the Witwatersrand
    INDEPTH Network, East Legon)

  • Kathleen Kahn

    (University of the Witwatersrand
    INDEPTH Network, East Legon)

  • Ryan G. Wagner

    (University of the Witwatersrand
    INDEPTH Network, East Legon)

  • Alisha N. Wade

    (University of the Witwatersrand)

  • Floidy Wafawanaka

    (University of the Witwatersrand)

  • F. Xavier Gómez-Olivé

    (University of the Witwatersrand
    INDEPTH Network, East Legon)

  • Rhian Twine

    (University of the Witwatersrand)

  • Zané Lombard

    (National Health Laboratory Service & University of the Witwatersrand)

  • Scott Hazelhurst

    (University of the Witwatersrand
    University of the Witwatersrand)

  • Ami S. Bhatt

    (Stanford University
    Stanford University
    Stanford University)

Abstract

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.

Suggested Citation

  • Fiona B. Tamburini & Dylan Maghini & Ovokeraye H. Oduaran & Ryan Brewster & Michaella R. Hulley & Venesa Sahibdeen & Shane A. Norris & Stephen Tollman & Kathleen Kahn & Ryan G. Wagner & Alisha N. Wade, 2022. "Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-021-27917-x
    DOI: 10.1038/s41467-021-27917-x
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