In 2007, the Human Microbiome Project set out to measure the human microbiome and its role in disease. Fast forward eighteen years, and we are excited to present what could be the largest cross-sectional and population-based survey of gut microbiome composition in relation to human health in low- and middle-income country (LMIC) populations:  the AWI-Gen Microbiome Project – a collaborative effort that builds on the foundational goals of earlier research. The second phase of this project explores the intricate relationships between gut microbiome composition, human health, and environmental factors across diverse LMICs in Africa.

Our study leveraged a network of health and demographic surveillance systems (HDSSs) in LMICs and the Developmental Pathways for Health Research Unit in Soweto, South Africa that support random cross-sectional population sampling. This approach provided an opportunity for the capture of population-level trends as each HDSS has engaged with host communities for over a decade, conducting engagement before study approval and through study conclusion, with a focus on the needs of the community. What we present in this study is from the second phase of the AWI-Gen Project. The pilot phase comprised just under 200 participants from two centres in South Africa1,2. In this phase, we randomly sampled 1,820 adults (1,801 women and 19 men) from well-characterized populations in six research centres from 2018 - 2023. The communities spanned  a range of settings (Figure 1), including:

• Rural, predominantly horticultural areas in Nanoro, Burkina Faso (BF), and Navrongo, Ghana (GH).

• Rapidly transitioning rural areas in Agincourt and DIMAMO, South Africa (SA).

• Urban industrial informal settlements in Viwandani and Korogocho in Nairobi, Kenya (KE).

Urban post-industrial settlements in Soweto, South Africa.Figure 1. A depiction of the studied communities. A&B: DIMAMO, South Africa; C&D: Soweto, South Africa; E&F: Nanoro, Burkina Faso; G&H: Agincourt; I&J: Nairobi, Kenya and K&L: Navrongo, Ghana.

The differences in these settings were accompanied by drastic differences in population density, water sanitation, access to healthcare and disease profiles (Table 1). In this study, we, therefore, aimed to shed light on how some of these factors influence microbiome diversity. 

Table 1. Site-level health and demographic summary statistics

Variability in microbiome composition

One of the main findings from our study is the significant association of geographical location on microbiome variation. Factors like population density and  access to health care and water sanitation  correlate  closely with alpha diversity and taxon prevalence. Notably, even sites with similar subsistence strategies and industrialization levels exhibited marked differences. For instance, while Bifidobacterium and Cryptobacteroides were similarly abundant in both Nairobi and Soweto, the levels of Prevotella, Bacteroides, and Phocaeicola in Nairobi closely resembled those typically found in rural areas.

Additionally, our study highlights the influence of migration patterns. Nairobi's informal settlements experience high rates of in- and out-migration, which significantly impacts the gut microbiome of local residents3,4. By integrating paired phenotype and metagenomic data, we were able to relate microbiome composition with information about diet and antibiotic exposure. This approach enabled us to identify features that define a diet-related nutrient niche supporting the persistence of T. succinifaciens and predicting antibiotic sensitivity that may lead to its loss.

Thousands of new viruses

Using the shotgun sequencing approach allowed for the identification of  40,135 novel viral genomes, including nine new and prevalent jumbophages. Notably, the identification of unidirectional gene organization in some of these jumbophages offers exciting avenues for future research, potentially indicating their integration into host genomes.

Insights into microbiome-HIV associations

Our study also delves into the microbiome's role in health disparities, particularly among people living with HIV (PLWH) in South Africa and Kenya. This represents one of the largest investigations into microbiome-HIV associations in these regions. Preliminary findings suggest that certain taxa are enriched in PLWH (women) receiving antiretroviral therapy (ART) compared to seronegative individuals, including taxa that have not been well-described in the context of HIV and inflammation. However, the exact nature of these associations remains unclear, underscoring the need for further exploration into how HIV infection, comorbidities, and lifestyle factors influence microbiome composition.

Community engagement, ethical and equitable research practices

As a highly collaborative project, the AWI-Gen Microbiome Project is committed to ethical and equitable research. It is important that our research priorities align with the community needs. To this end, the various study centres held consultative meetings with the community before the study commenced and at different stages through community advisory groups, community representatives,  and tribal leaders, though the COVID-19 outbreak limited meetings in some sites. Local field workers were hired to facilitate participant recruitment, ensuring a sound understanding of the study objectives that empowered them to confidently respond to participant questions (Figure 2). 

Figure 2. Interactions with the local communities and training sessions. A: A feedback session at a Nairobi site; B: A field visit in Agincourt, South Africa; C&D: Training sessions at South African and Kenyan institutes, respectively.

As the study progressed and local research needs were identified, relevant training workshops were organized with participation extending to other African research institutions and universities (Figure 2). This collaboration between Stanford University and the University of the Witwatersrand continues to evolve and presents a learning experience that we believe exemplifies how equitable research can lead to robust scientific outcomes that benefit all stakeholders. It has also been a fertile ground for trainees on both sides of the collaboration.

Conclusion

Advances in our understanding of the gut microbiome are gradually unfolding, particularly within African populations. This study significantly contributes to expanding the gut microbiome atlas, elucidating some of the intricate relationships between subsistence, industrialization, and lifestyle factors that shape our microbiomes. It is an important step toward grasping how the microbiome interacts with health and environmental contexts in diverse communities.

At the heart of the AWI-Gen Microbiome Project is a commitment to engaging local communities. As such, this study emphasizes the importance of consultation and collaboration, ensuring that the perspectives and needs of the communities involved are prioritized. This approach not only enriches the research but also fosters valuable knowledge exchange among researchers and trainees.

As we delve deeper into this fascinating field, the insights gained will help us better understand the complexities of human health and the vital role our microbiomes play in it across different populations. 

References

1. Oduaran, O. H. et al. Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. BMC Microbiol. 20, 330 (2020).
2. Tamburini, F. B. et al. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nat. Commun. 13, 926 (2022).
3. Beguy, D. et al. Health & Demographic Surveillance System Profile: The Nairobi Urban Health and Demographic Surveillance System (NUHDSS). Int. J. Epidemiol. 44, 462–471 (2015).
4. Beguy, D., Bocquier, P. & Zulu, E. M. Circular migration patterns and determinants in Nairobi slum settlements. Demogr. Res. 23, 549–586 (2010).