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Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and 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 th...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8863827/ https://www.ncbi.nlm.nih.gov/pubmed/35194028 http://dx.doi.org/10.1038/s41467-021-27917-x |
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author | Tamburini, Fiona B. Maghini, Dylan Oduaran, Ovokeraye H. Brewster, Ryan Hulley, Michaella R. Sahibdeen, Venesa Norris, Shane A. Tollman, Stephen Kahn, Kathleen Wagner, Ryan G. Wade, Alisha N. Wafawanaka, Floidy Gómez-Olivé, F. Xavier Twine, Rhian Lombard, Zané Hazelhurst, Scott Bhatt, Ami S. |
author_facet | Tamburini, Fiona B. Maghini, Dylan Oduaran, Ovokeraye H. Brewster, Ryan Hulley, Michaella R. Sahibdeen, Venesa Norris, Shane A. Tollman, Stephen Kahn, Kathleen Wagner, Ryan G. Wade, Alisha N. Wafawanaka, Floidy Gómez-Olivé, F. Xavier Twine, Rhian Lombard, Zané Hazelhurst, Scott Bhatt, Ami S. |
author_sort | Tamburini, Fiona B. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8863827 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-88638272022-03-17 Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa Tamburini, Fiona B. Maghini, Dylan Oduaran, Ovokeraye H. Brewster, Ryan Hulley, Michaella R. Sahibdeen, Venesa Norris, Shane A. Tollman, Stephen Kahn, Kathleen Wagner, Ryan G. Wade, Alisha N. Wafawanaka, Floidy Gómez-Olivé, F. Xavier Twine, Rhian Lombard, Zané Hazelhurst, Scott Bhatt, Ami S. Nat Commun Article 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. Nature Publishing Group UK 2022-02-22 /pmc/articles/PMC8863827/ /pubmed/35194028 http://dx.doi.org/10.1038/s41467-021-27917-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Tamburini, Fiona B. Maghini, Dylan Oduaran, Ovokeraye H. Brewster, Ryan Hulley, Michaella R. Sahibdeen, Venesa Norris, Shane A. Tollman, Stephen Kahn, Kathleen Wagner, Ryan G. Wade, Alisha N. Wafawanaka, Floidy Gómez-Olivé, F. Xavier Twine, Rhian Lombard, Zané Hazelhurst, Scott Bhatt, Ami S. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa |
title | Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa |
title_full | Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa |
title_fullStr | Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa |
title_full_unstemmed | Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa |
title_short | Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa |
title_sort | short- and long-read metagenomics of urban and rural south african gut microbiomes reveal a transitional composition and undescribed taxa |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8863827/ https://www.ncbi.nlm.nih.gov/pubmed/35194028 http://dx.doi.org/10.1038/s41467-021-27917-x |
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