Expanding the human gut microbiome atlas of Africa

Study information

Reviewed Marked as Reviewed by Svetlana up on 2025-2-13

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

39880958

DOI Digital object identifier for electronic documents.

10.1038/s41586-024-08485-8

URI

Authors

Maghini DG, Oduaran OH, Olubayo LAI, Cook JA, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Wirbel J, Bhatt AS, Hazelhurst S

Journal

Nature

Year

2025

Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives1, are not equitably represented in large-scale gut microbiome research2-4. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-2-13

Curated date: 2025/02/03

Curator: Taofeecoh

Revision editor(s): WikiWorks, Taofeecoh

Subjects

Location of subjects: Kenya; South Africa

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV-

Group 1 name Corresponds to the case (exposed) group for case-control studies: People Living With HIV on Antiretroviral therapy (ART+ PLWH)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Women living with HIV in Agincourt, South Africa (n = 60), Soweto, South Africa (n = 50) and Nairobi, Kenya (n = 19)

Group 0 sample size Number of subjects in the control (unexposed) group: 719

Group 1 sample size Number of subjects in the case (exposed) group: 119

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Statistical Analysis

Statistical test: Mixed-Effects Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.01

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: antibiotic therapy, geographic area

Alpha Diversity

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: decreased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-13

Curated date: 2025/02/05

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

Source: Figure 4d, Supplementary Data 10

Description: Species-level prokaryotic differential abundance between seronegative and HIV+ participants in Agincourt (South Africa), Soweto (South Africa) and Nairobi (Kenya).

Abundance in Group 1: increased abundance in People Living With HIV on Antiretroviral therapy (ART+ PLWH)

NCBI	Quality Control	Links
Acidaminococcus massiliensis
Bacteroides ovatus
Bacteroides sp.
Blautia massiliensis (ex Durand et al. 2017)
Cloacibacillus porcorum
Clostridium sp. CAG:58
Dielma fastidiosa
Dorea longicatena
Dysosmobacter welbionis
Enterocloster bolteae
Enterocloster citroniae
Eubacteriales incertae sedis
Flavonifractor plautii
Fusobacterium mortiferum
Gemella sanguinis
Mailhella massiliensis
Megamonas funiformis
Oscillibacter sp.
Parabacteroides distasonis
Paraprevotella clara
Paraprevotella xylaniphila
Phocaeicola
Phocaeicola massiliensis
Pyramidobacter piscolens
Ruminococcus sp.
Streptococcus parasanguinis
Streptococcus salivarius
Streptococcus sanguinis
Streptococcus sp.
Streptococcus sp. HMSC067H01
Thomasclavelia saccharogumia
[Ruminococcus] torques
[Ruminococcus] torques ATCC 27756
Candidatus Caccocola faecigallinarum
Pandoraea faecigallinarum
Firmicutes bacterium CAG:137
Merdibacter massiliensis
Clostridium sp. CAG:7
Sutterella sp. CAG:521

Revision editor(s): Taofeecoh, WikiWorks

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-13

Curated date: 2025/02/07

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

Source: Supplementary Data 10

Description: Species-level prokaryotic differential abundance between seronegative and HIV+ participants in Agincourt (South Africa), Soweto (South Africa) and Nairobi (Kenya).

Abundance in Group 1: decreased abundance in People Living With HIV on Antiretroviral therapy (ART+ PLWH)

NCBI	Quality Control	Links
Bifidobacterium adolescentis
Bifidobacterium ruminantium
Candidatus Geddesella stercoravicola
Christensenellaceae bacterium
Clostridia bacterium
Clostridiaceae bacterium AF97-07pH10A
Clostridiales bacterium
Clostridium sp. CAG:1193
Clostridium sp. CAG:226
Clostridium sp. CAG:349
Clostridium sp. CAG:433
Clostridium sp. CAG:448
Coprobacter fastidiosus
Anaerovoracaceae
Faecalibacterium longum
Faecalibacterium prausnitzii
Faecalibacterium sp. CAG:82
Firmicutes bacterium CAG:124
Firmicutes bacterium CAG:129
Firmicutes bacterium CAG:238
Lachnospiraceae bacterium
Mycoplasma sp. CAG:611
Oscillibacter sp.
Oscillospiraceae bacterium
Ruminococcus sp. CAG:382
Segatella hominis
unclassified Bacillota
unclassified Bacillus (in: firmicutes)
unclassified Bacteroidales
unclassified Clostridia
unclassified Anaerovoracaceae Incertae Sedis
unclassified Clostridium
unclassified Eubacteriales
unclassified Faecalibacterium
unclassified Lachnospiraceae
unclassified Oscillibacter
unclassified Oscillospiraceae
unclassified Dehalococcoidales

Revision editor(s): Taofeecoh, WikiWorks