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City-slicker or rural farmer? What the bugs in your gut can tell you about your health

- Wits University

Scientists have for the first time described the microbiome in SA individuals in ‘city’ and ‘rural’ populations and discovered new bacteria in SA microbiomes.

Gut microbiome refers to the trillions of microorganisms and their genetic material that live in your intestinal tract.

These microbes influence health and disease in a range of ways, from gastrointestinal infection, to inflammatory bowel disease, to vaccine efficacy. 

These microorganisms, mainly comprising bacteria, include the good, the potentially bad, and the bad bugs. An imbalance in the proportion of these bugs have been reported to be associated with several diseases including obesity, which is a global health burden and precursor to many debilitating conditions.

If we don’t know what a normal, healthy microbiome looks like, we can’t know whether or how the microbiome is changing because of disease or in response to medicine.

Weighty worries in the West

However, most microbiome research to date has focused on individuals living in western nations, or the Global North, while the microbiome of much of the world’s population remains undescribed.

“This is a problem because we know that microbiome varies due to lifestyle, diet, and environment, so what we learn from studying the microbiome in western individuals may not be applicable to other populations, including those undergoing lifestyle changes,” says Dr Ovokeraye Oduaran from the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at Wits and co-author of the study.

“Access to fast foods and more ‘westernized’ lifestyles are likely contributing to changes in the microbiome in people all over the world.”

SA gut microbiome is transitional

The study, published in Nature Communications on 22 February 2022, describes the microbiome in South African individuals in ‘city’ and ‘rural’ populations, in great depth, for the first time.

Scientists highlighted the transitional state of South African microbiomes, which reflects the gradual shift towards more westernized dietary and lifestyle practices.

“Understanding what happens to these bugs that have such an impact on human wellbeing, as we navigate this intermediate space, provides us with insights into the differences we see between very traditional populations and their highly westernized counterparts,” says Oduaran.

This is important because the proportions of the different microorganisms in our bodies can be indicators of dietary and lifestyle patterns, and consequently health statuses.

On a local scale, they found the more industrialized ‘city’ inhabitants in South Africa to have microbiomes that are more closely related to the microbiomes of individuals living in the US and Western Europe compared to South Africans living in more rural areas. Globally, however, the gut microbiota of South African participants was in several respects ‘intermediate’ between those of ‘western’ cohorts and cohorts of participants practicing traditional/subsistence lifestyles.

“Despite this intermediate state, South African microbiomes do not exclusively conform to being ‘in between’ the microbiomes of western and very traditional populations,” says Oduaran, highlighting the need for more globally representative studies.

The results suggest that the gut microbiome in South African populations do not exist along a simple 'western-nonwestern' axis and that these populations contain microbial diversity that remains to be described.

New gut bacteria unearthed in SA

Excitingly, South African microbiomes contained some microbes that couldn’t be identified because they don't exist in available microbial genome reference collections. “These bacteria had never been discovered before” says Professor Ami Bhatt, a co-author at Stanford University. “We discovered totally new bacteria living in the gut microbiome, using exciting new DNA sequencing technologies.”

This successful pilot study provides the basis for more expansive studies. In future, Wits and Stanford researchers will continue to collaborate to move this project to the next phase and describe the microbiome of a greater number of participants from additional diverse populations.

Scientists at the SBIMB collaborated with Wits partners at the Developmental Pathways to Health Research Unit (DPHRU), the Medical Research Council-Wits Rural Public Health and Health Transitions Research Unit (Agincourt), the Division of Human Genetics, School of Electrical and Information Engineering, and scientists at the Bhatt Lab at Stanford University.