Over 40,000 new gut microbes discovered in African populations

More than 40,000 previously unknown gut microbes in African populations could completely change how medicines work for millions of people, according to scientists.

Research led by the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at the University of the Witwatersrand, South Africa, addressed the gap in microbiome studies, which have largely overlooked African populations.

The long-term goal is to be able to translate a lot of this into real life. We want to make sure that when medicines are made, as many people as possible are counted."

Ovokeraye Oduaran, one of the researchers

Why this matters

For years, most medicines have been developed based on research from high-income countries. But the gut bacteria - the tiny organisms living in the digestive systems - help process these medicines, and African populations have completely different gut bacteria to people in Europe or America.

This means many drugs might not work the same way for African patients. The researchers say their findings, published in the journal Nature could help create better treatments specifically designed for African populations.

“That’s how important these studies are and it gives you that power to be able to make that decision,” says Luicer Ingasia Olubayo, a Sydney Brenner Charitable Trust postdoctoral fellow at SBIMB, who also worked on the study.

She says doctors might need to prescribe different medication or add probiotics when treating African patients.

Surprise discoveries

The team from the Sydney Brenner Institute found more than 1,000 new bacteria species and over 40,000 new viruses living in the gut microbiomes of African people.

“We found a lot of novelties,” says Olubayo.

“Certain bacteria that were rare on other continents were plentiful in Africa.”

The researchers collected stool samples from about 1,800 women across Kenya, Ghana, Burkina Faso, and South Africa. These samples were analysed using genetic sequencing technology to identify the different microorganisms present.

New hope for HIV treatment

One of the most exciting discoveries was finding unique gut bacteria patterns in people with HIV, say the researchers.

“Had we not done this study, we would not have found this unique microbial signature linked to HIV infection,” says Olubayo, explaining that the bacteria patterns they found were completely different from those seen in HIV patients in wealthier countries.

This discovery could lead to better ways to detect, monitor, and treat HIV in African populations.

The study was the largest ever to investigate the microbiomes of women living with HIV and  understanding this disease requires regional-specific research.

City vs. rural life

The researchers found that people living in rural areas had richer, more diverse gut bacteria than city dwellers. They also found that urban participants often lacked a bacteria called Treponema, probably because they eat less fibre and use more antibiotics.

Charissa Naidoo, co-director of the African Microbiome Institute, warns that beneficial gut bacteria are disappearing as more Africans adopt urban lifestyles and use more antibiotics.

“Urgent action, such as through nutritional intervention, is needed to preserve gut microbiome diversity in the era of antibiotic overuse,” she cautions.

This loss of diversity could have long-term health consequences, potentially contributing to increases in allergies, autoimmune disorders, and metabolic diseases like diabetes.

However, the story isn’t as simple as “rural versus urban”. The team found that gut bacteria varied significantly even between different cities like those in Kenya versus South Africa.

“We questioned the rural-urban dichotomy that is usually used by other researchers,” explains Olubayo. “Instead, there was fluidity and transition between these populations.”

This suggests that local diets, environmental factors, and cultural practices all play important roles in shaping our gut microbiome.

Filling in the blank spots

In 2007, the US National Institutes of Health launched a major global project called the Human Microbiome Project, to improve understanding of the microbiota involved in human health and disease.

However, most studies in this area have largely focused on high-income populations, with low- and middle-income countries severely underrepresented.

“If you look at the map of the world and plot how many population-based studies have been done, Africa is ending up to be blank, so we’re happy that we are able to paint the African map as well,” says Olubayo.

The researchers say they are expanding their work to study connections between gut bacteria and other health issues like sleep problems, menopause, and brain diseases.

Naidoo, of the African Microbiome Institute, suggests future research should also focus on tuberculosis, given its widespread impact in South Africa and neighbouring countries.

Jerolen Naidoo, senior researcher in bioengineering and integrative genomics at the Council of Scientific and Industrial Research, says this work is the first large-scale study of its kind, led by and focusing on Africans.

“These findings represent a watershed moment for the African human microbiome by highlighting the scale of novel biodiversity that still exists within African microbiomes,” he says.

More equitable representation of this diversity is needed within global resources and reference databases, he adds.