The University of Southampton
×
Filter your search:
University of Southampton Institutional Repository

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

Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa
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 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.
2041-1723
Tamburini, Fiona B.
8b0fe9e7-ae56-4bb7-9577-7ac49972a8f0
Maghini, Dylan
1da6e7c3-d778-4454-a9c0-8509e7299eaa
Oduaran, Ovokeraye
a42d0679-3f49-4f2d-81ee-9fbbb1dda4df
Brewster, Ryan
e5368dc7-1ade-4ecd-be36-1c24025947b1
Hulley, Michaella R.
4c47d670-1543-4f0b-ad88-e29a028d633f
Sahibdeen, Venesa
bdccb4b5-a572-4824-be64-6d9a2e466d57
Norris, Shane A.
1d346f1b-6d5f-4bca-ac87-7589851b75a4
Tollman, Stephen
25a01ce2-eeab-4401-997f-6b701349f6ec
Kahn, Kathleen
e8f0af52-65ce-4744-b029-688db6e12dff
Wagner, Ryan G.
03a17360-393e-4d3c-a35f-963d72025403
Wade, Alisha N.
7d929a5e-114b-4499-bde4-b1047a611f26
Wafawanaka, Floidy
50891b35-8b1b-4cf9-ae34-8ec5d57dc967
Gómez-Olivé, F. Xavier
4d518042-0358-44e3-b4cb-ddf482a86a49
Twine, Rhian
c4830e46-191a-4f9d-92a0-a2e1a0cc9541
Lombard, Zané
42a83197-436e-470d-b223-4cddc7adf8e7
Agongo, Godfred
0d335cba-7025-45bb-bb5b-86c09c2ee944
Alberts, Marianne
0081268a-e11f-4845-942f-1d73ec785983
Ali, Stuart
7a81b060-49ee-43f2-89d9-a7ea0a1e3e16
Asiki, Gershim
3d94a82b-3397-4d51-bb73-e455a73f5daa
Baloyi, Vukosi
a085c567-4dcd-4e48-a286-efbb9493fa01
Boua, Palwendé Romuald
4b08fe0e-4c96-4f55-ac1f-9048a777ebcf
Brandenburg, Jean-Tristan
e6c68784-d595-4242-8afc-98430590eeb4
Ceballos, Francisco Camiña
f1451006-adf9-4f4e-a496-3bbb2787acb5
Chikowore, Tinashe
b53b1cb9-8363-4e2c-9d62-dc3a8627a7b5
Choma, Solomon
2a7a391c-cd60-4ede-a10e-bddee9853d0d
Choudhury, Ananyo
f9eee613-a754-439b-a028-fdd7ebca55e5
Crowther, Nigel
ca4aa5ba-4f92-4c4d-9736-1dcf303dee40
Debpuur, Cornelius
86cc89d7-984e-4a7b-8130-5461a00d2bec
Gondwe, Mwawi
0f5a4d03-d61c-4013-9d53-6371cae4a448
Hazelhurst, Scott
329cfaab-4b17-4b64-bdba-da4d916777ec
Kahn, Kathleen
e8f0af52-65ce-4744-b029-688db6e12dff
Khayeka-Wandabwa, Christopher
80956989-2ece-472c-80af-484a32685aeb
Kisiangani, Isaac
32b2b57d-16f0-4529-9273-df082705bf98
Kyobutungi, Catherine
dc9572b9-0eb2-4688-9101-d73ce9ebcd0a
Lombard, Zané
42a83197-436e-470d-b223-4cddc7adf8e7
Mashaba, Given
3549fe71-f5d9-453b-a7bc-2ef1494ebc80
Mashinya, Felistas
3ae5087d-b601-4602-890f-e8ea586fdaad
Mathema, Theo
0004a8f9-1402-4aca-ad9e-86bd063e5c6e
Micklesfield, Lisa
4c625289-a9ed-47e1-8dec-a1d445481206
Mohamed, Shukri
6340f3f1-0e61-4b52-adea-19b980ec0723
Mthembu, Busisiwe
c7a0e73f-e242-44c0-8272-aaac9d8806be
Mukomana, Freedom
33797069-81d1-4745-82f3-6a56a3e39bed
Nonterah, Engelbert
09395d6c-a296-4216-a0cf-0b4c75c6de3f
Norris, Shane A.
1d346f1b-6d5f-4bca-ac87-7589851b75a4
Oduaran, Ovokeraye
a42d0679-3f49-4f2d-81ee-9fbbb1dda4df
Oduro, Abraham R.
dd6fc6ff-5927-48bc-abfb-d572eb3da430
Gómez-Olivé, F. Xavier
4d518042-0358-44e3-b4cb-ddf482a86a49
Ramsay, Michèle
75c868d6-bac7-4db2-b611-d498ab0d12fc
Sankoh, Osman
643b449d-5278-49a5-8470-45d06eda6923
Sengupta, Dhriti
698f82dc-9f62-4ea1-b716-7ee02ebc53ab
AWI-Gen and the H3Africa Consortium
Tamburini, Fiona B.
8b0fe9e7-ae56-4bb7-9577-7ac49972a8f0
Maghini, Dylan
1da6e7c3-d778-4454-a9c0-8509e7299eaa
Oduaran, Ovokeraye
a42d0679-3f49-4f2d-81ee-9fbbb1dda4df
Brewster, Ryan
e5368dc7-1ade-4ecd-be36-1c24025947b1
Hulley, Michaella R.
4c47d670-1543-4f0b-ad88-e29a028d633f
Sahibdeen, Venesa
bdccb4b5-a572-4824-be64-6d9a2e466d57
Norris, Shane A.
1d346f1b-6d5f-4bca-ac87-7589851b75a4
Tollman, Stephen
25a01ce2-eeab-4401-997f-6b701349f6ec
Kahn, Kathleen
e8f0af52-65ce-4744-b029-688db6e12dff
Wagner, Ryan G.
03a17360-393e-4d3c-a35f-963d72025403
Wade, Alisha N.
7d929a5e-114b-4499-bde4-b1047a611f26
Wafawanaka, Floidy
50891b35-8b1b-4cf9-ae34-8ec5d57dc967
Gómez-Olivé, F. Xavier
4d518042-0358-44e3-b4cb-ddf482a86a49
Twine, Rhian
c4830e46-191a-4f9d-92a0-a2e1a0cc9541
Lombard, Zané
42a83197-436e-470d-b223-4cddc7adf8e7
Agongo, Godfred
0d335cba-7025-45bb-bb5b-86c09c2ee944
Alberts, Marianne
0081268a-e11f-4845-942f-1d73ec785983
Ali, Stuart
7a81b060-49ee-43f2-89d9-a7ea0a1e3e16
Asiki, Gershim
3d94a82b-3397-4d51-bb73-e455a73f5daa
Baloyi, Vukosi
a085c567-4dcd-4e48-a286-efbb9493fa01
Boua, Palwendé Romuald
4b08fe0e-4c96-4f55-ac1f-9048a777ebcf
Brandenburg, Jean-Tristan
e6c68784-d595-4242-8afc-98430590eeb4
Ceballos, Francisco Camiña
f1451006-adf9-4f4e-a496-3bbb2787acb5
Chikowore, Tinashe
b53b1cb9-8363-4e2c-9d62-dc3a8627a7b5
Choma, Solomon
2a7a391c-cd60-4ede-a10e-bddee9853d0d
Choudhury, Ananyo
f9eee613-a754-439b-a028-fdd7ebca55e5
Crowther, Nigel
ca4aa5ba-4f92-4c4d-9736-1dcf303dee40
Debpuur, Cornelius
86cc89d7-984e-4a7b-8130-5461a00d2bec
Gondwe, Mwawi
0f5a4d03-d61c-4013-9d53-6371cae4a448
Hazelhurst, Scott
329cfaab-4b17-4b64-bdba-da4d916777ec
Kahn, Kathleen
e8f0af52-65ce-4744-b029-688db6e12dff
Khayeka-Wandabwa, Christopher
80956989-2ece-472c-80af-484a32685aeb
Kisiangani, Isaac
32b2b57d-16f0-4529-9273-df082705bf98
Kyobutungi, Catherine
dc9572b9-0eb2-4688-9101-d73ce9ebcd0a
Lombard, Zané
42a83197-436e-470d-b223-4cddc7adf8e7
Mashaba, Given
3549fe71-f5d9-453b-a7bc-2ef1494ebc80
Mashinya, Felistas
3ae5087d-b601-4602-890f-e8ea586fdaad
Mathema, Theo
0004a8f9-1402-4aca-ad9e-86bd063e5c6e
Micklesfield, Lisa
4c625289-a9ed-47e1-8dec-a1d445481206
Mohamed, Shukri
6340f3f1-0e61-4b52-adea-19b980ec0723
Mthembu, Busisiwe
c7a0e73f-e242-44c0-8272-aaac9d8806be
Mukomana, Freedom
33797069-81d1-4745-82f3-6a56a3e39bed
Nonterah, Engelbert
09395d6c-a296-4216-a0cf-0b4c75c6de3f
Norris, Shane A.
1d346f1b-6d5f-4bca-ac87-7589851b75a4
Oduaran, Ovokeraye
a42d0679-3f49-4f2d-81ee-9fbbb1dda4df
Oduro, Abraham R.
dd6fc6ff-5927-48bc-abfb-d572eb3da430
Gómez-Olivé, F. Xavier
4d518042-0358-44e3-b4cb-ddf482a86a49
Ramsay, Michèle
75c868d6-bac7-4db2-b611-d498ab0d12fc
Sankoh, Osman
643b449d-5278-49a5-8470-45d06eda6923
Sengupta, Dhriti
698f82dc-9f62-4ea1-b716-7ee02ebc53ab

AWI-Gen and the H3Africa Consortium (2022) Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nature Communications, 13, [926]. (doi:10.1038/s41467-021-27917-x).

Record type: Article

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.

This record has no associated files available for download.

More information

Published date: 22 February 2022

Identifiers

Local EPrints ID: 504742
URI: http://eprints.soton.ac.uk/id/eprint/504742
DOI: doi:10.1038/s41467-021-27917-x
ISSN: 2041-1723
PURE UUID: ae72156f-f74f-4eb1-9b2d-783e3539efd6
ORCID for Shane A. Norris: ORCID iD orcid.org/0000-0001-7124-3788
ORCID for Shane A. Norris: ORCID iD orcid.org/0000-0001-7124-3788

Catalogue record

Date deposited: 18 Sep 2025 16:57
Last modified: 19 Sep 2025 02:02

Export record

Altmetrics

Contributors

Author: Fiona B. Tamburini
Author: Dylan Maghini
Author: Ovokeraye Oduaran
Author: Ryan Brewster
Author: Michaella R. Hulley
Author: Venesa Sahibdeen
Author: Shane A. Norris ORCID iD
Author: Stephen Tollman
Author: Kathleen Kahn
Author: Ryan G. Wagner
Author: Alisha N. Wade
Author: Floidy Wafawanaka
Author: F. Xavier Gómez-Olivé
Author: Rhian Twine
Author: Zané Lombard
Author: Godfred Agongo
Author: Marianne Alberts
Author: Stuart Ali
Author: Gershim Asiki
Author: Vukosi Baloyi
Author: Palwendé Romuald Boua
Author: Jean-Tristan Brandenburg
Author: Francisco Camiña Ceballos
Author: Tinashe Chikowore
Author: Solomon Choma
Author: Ananyo Choudhury
Author: Nigel Crowther
Author: Cornelius Debpuur
Author: Mwawi Gondwe
Author: Scott Hazelhurst
Author: Kathleen Kahn
Author: Christopher Khayeka-Wandabwa
Author: Isaac Kisiangani
Author: Catherine Kyobutungi
Author: Zané Lombard
Author: Given Mashaba
Author: Felistas Mashinya
Author: Theo Mathema
Author: Lisa Micklesfield
Author: Shukri Mohamed
Author: Busisiwe Mthembu
Author: Freedom Mukomana
Author: Engelbert Nonterah
Author: Shane A. Norris ORCID iD
Author: Ovokeraye Oduaran
Author: Abraham R. Oduro
Author: F. Xavier Gómez-Olivé
Author: Michèle Ramsay
Author: Osman Sankoh
Author: Dhriti Sengupta
Corporate Author: AWI-Gen and the H3Africa Consortium

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Library staff additional information
Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×