Africa’s largest human microbiome study sheds light on gut diversity and health

The most extensive study of the gut microbiome in Africa has discovered new microbial species and never-before-reported metagenomes* from several African sites.

The paper, titled, Expanding the human gut microbiome atlas of Africa, was published today in Nature, the world’s leading scientific journal.

The gut microbiome has a significant impact on human health, and the lack of knowledge of the diversity of microbiomes in Africa has been a barrier to future health interventions and research. 

The study is a critical development in gut health research globally as much more can now be learned, particularly about diseases such as cancer, diabetes, and obesity, and their relationship to gut microbiota. 

In the study, high-quality genomes of 1,005 bacterial and 40,135 viral species have been produced, which bolsters the information in the current human gut microbiome databases. 

“The importance of the microbiome on health is one of the most revolutionary scientific insights in the last 15 years. There are likely as many bacteria in the gut as there are human cells and more genetic diversity in the gut than in the human DNA,” says co-author Professor Scott Hazelhurst, senior scientist at the Sydney Brenner Institute for Molecular Bioscience (SBIMB) and Professor of Bioinformatics in the School of Electrical and Information Engineering, Wits University. 

Healthy gut microbiome plays a key role in overall health, helping with nutrient absorption, drug metabolism, gut barrier integrity, immune function, and protection against harmful disease pathogens.

Geographical location determines gut health

Participants in the study were from different regions and led varied lifestyles, including rural farming communities, towns transitioning towards industrialization, and dense urban settlements. 

“This has rarely been captured in microbiome studies. We now know that geography largely shapes microbiome differences, with some species thriving in rural areas and others in industrialised settings,” says co-author Dr Luicer Ingasia Olubayo of the SBIMB.

Food deserts highlight impact of absence of beneficial gut microbiota in urban settings 

In particular, there is the absence of important bacteria, Treponema, in urban participants. This is likely because of urbanisation, overuse of antibiotics, and so-called food deserts.

Food deserts are areas with an abundance of affordable, calorie-dense food but fewer fresh, healthy foods (which are often more expensive). People living in food deserts have a higher risk of developing diabetes, heart disease, and obesity. 

“Interestingly, in Burkina Faso, where a traditional lifestyle is led, there are more diverse gut microbiota associated with healthier strains of bacteria. Burkina Faso is not without its health challenges, particularly a high burden of infectious diseases. But people are eating more healthily,” says Hazelhurst. 

Studies in low- and middle-income countries and non-industrialised communities, such as hunter-gatherer groups, show that the microbiome compositions of these populations are distinct from those in high-income country research cohorts.

Precision medicine and health interventions must be site and region-specific

Africa contains the most extraordinary genetic diversity, and the study shows the importance of African genomic data for furthering science and health research. “Africa is understudied, but with new information, we know that health and precision medicine interventions should be site and region-specific. It can’t be a one-size-fits-all approach to gut health,” explains Professor Michèle Ramsay, SBIMB Director. 

Despite its large size, the study includes only four countries, so it represents just a fraction of Africa’s vast ecological and cultural diversity.

Moreover, the study’s HIV-related findings highlight the importance of studying microorganisms linked to health. “This research also underscores the need to include low-and-middle-income countries in global microbiome studies for more representative and applicable results,” says Olubayo. 

Hazelhurst notes the importance of healthy lifestyle habits, like eating high-fibre foods, avoiding ultra-processed food, and taking antibiotics only when necessary. He suggests simple changes, such as diluting fruit juices with water, eating brown rather than white bread, and reading food labels. “If the labels have words that are hard to understand, then the food may contain additives that  are not good for your gut microbiota.”

Logistical feats and shotgun sequencing – the power of collaboration and advanced technology

After consultation with local communities, local field workers and scientists collected stool, blood, and urine samples, clinical information, and questionnaire responses. Samples from across regions (some more than 16 000 km apart) were then sent to SBIMB’s Biobank in South Africa and stored at -80° Celsius. 

“A defining feature of the study was the transformative potential of a collaborative and community-engaged research framework,” says co-author Dr Ovokeraye Oduaran at the SBIMB. The process of giving participants feedback on their results has started.

Meanwhile, the study made use of ‘shotgun sequencing,’ which has more power in identifying less abundant ‘taxa’**  in the gut microbiome than the use of 16s genetic sequencing. This data gives more biologically meaningful results.

The study expands our knowledge of urban and rural gut microbiomes

This study, by markedly developing the knowledge of urban and rural microbiomes in Africa, represents a key step in extending our understanding of the composition, functions, and diversity of the gut microbiota on a global scale. 

“This is also the beginning of many possibilities. There are plans to investigate the interplay between the microbiome, host genetics, environmental exposures, and a wide range of chronic illnesses. We also intend to use new DNA sequencing techniques to examine antibiotic resistance, mobile genetic elements, and the stability and dynamics of viruses that infect bacteria,” says Olubayo. 

*A metagenome is the collection of all genetic material (DNA) from a community of microorganisms in a specific environment. Instead of studying just one microbe at a time, scientists analyse all the microbes present in the human gut to  understand their diversity and functions.

** Scientists use taxa to describe and categorise the different bacteria, viruses, fungi, and other microbes living in the gut, helping to understand their roles in digestion, immunity, and overall health.

The research paper was a sub-study of a multi-institution initiative under the umbrella of the Human Heredity and Health in Africa (H3Africa) consortium, the Wits-INDEPTH Partnership for Genomic Studies (AWI-Gen) and Stanford University in the US. The AWI-Gen collaboration centres were the Clinical Research Unit of Nanoro, Burkina Faso; the Navrongo Health Research Centre, Ghana; the DIMAMO Population Health Research Centre, University of Limpopo; the MRC/Wits Developmental Paths for Health Research Unit (DPHRU); the MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt); and the SBIMB at Wits University, South Africa. Dr Dylan Maghini, a joint postdoctoral fellow at the SBIMB and Stanford University and Dr Ovokeraye Oduaran led the paper.