In a call to action to policymakers and scholars on the continent, a group of mostly African microbiologists have highlighted the importance of urgently increasing research into Africa’s woefully understudied microbiomes – microbial communities found in soils, water, plants and the guts of animals and humans.

Africa is trailing behind in efforts to meet the United Nations’ 17 sustainable development goals (SDGs) but could catch up quickly by closing the gaps in scientific knowledge of the continent’s microbiomes.

“African biomes are much neglected and previous studies have disproportionately focused on the Global North. There are clear gaps in the current understanding of microbiomes from the Global South, in general, and Africa specifically,” say the group of scientists from Benin, Cote d’Ivoire, Ghana, Morocco, Nigeria, South Africa, the United Kingdom and Zimbabwe, writing in the June 2023 edition of the top-rated international journal Nature Reviews Microbiology.

The lead author of the commentary piece, titled ‘African microbiomes matter’, is Professor Thulani P Makhalanyane, holder of the DSI/NRF SARChI in Marine Microbiomics in the University of Pretoria’s Department of Biochemistry, Genetics and Microbiology.

The missing link: microbiomes and the SDGs

Pointing out that microbiomes underpin virtually all ecosystem services that are of benefit to humans, the scientists emphasise that a robust understanding of microbiomes is essential to attain the SDGS.

However, African biomes, which are believed to be unique, are underexplored.

These knowledge gaps complicate efforts to “disentangle” the genetic diversity of African microbial communities and their contribution to human health, biodiversity, agriculture and conservation.

For example, an analysis of agriculture in Africa reveals generally low productivity compared to developed countries. According to the “African biomes matter” commentary article, this is likely due to a combination of biotic and abiotic factors, such as soil fertility, unchecked pathogen attacks owing to a lack of surveillance, high salinity, increased incidents of droughts and inefficient management practices.

Despite this, Africa’s croplands still have an immense potential to feed an increasing population, especially given the crucial role that beneficial microorganisms play in plant growth and crop productivity.

“There is some evidence showing that African ecosystems are some of the most genetically diverse,” the scientists say. This is important because genetic diversity can strengthen resistance to pests, diseases and climate stressors.

Connecting diets, the gut biome and health care

Similarly, population studies have shown that Africans have higher genetic diversity than non-Africans, and that African diets vary substantially from those in the Global North. African diets tend to have a greater reliance on fermented foods, for example. This is likely to result in substantially varied gut microbiome, which may also harbour as yet undiscovered probiotics.

These and other differences, including communal lifestyles and eating habits (such as chewing sticks for oral hygiene) may directly impact gut microbiota. “Given recent efforts aimed at developing ‘precision medicine’, these differences may have implications in the development of health care tailored for Africans,” say Prof Makhalanyane and his co-authors.

“We urgently need to understand the implications of this genetic diversity and the connection between plant, animal and human populations in Africa. Such insights are crucial in efforts to attain the SDGs and explore African indigenous knowledge.”

Urgent steps required to close the knowledge deficit

Given the research backlogs in Africa, there is an urgent need to launch coordinated surveys of African microbiomes. To catch up, governments and researchers should focus on three main priorities: strengthening research networks on the African continent, developing science plans and policy documents on microbiome research (which most African countries lack), and establishing regional infrastructure hubs to support microbiome science.

Currently, networks of African scientists associated with the African Microbiome Programme (AMP), led by Prof Makhalanyane, are working to develop Microbiome Centres of Excellence in West Africa, East Africa, North Africa and Southern Africa. The AMP is a project established to help provide insights on African microbiome.  

“Under the AMP, we have launched a plan to sequence 10 million samples, including soils, water, plants, humans and animals from the African continent,” say the writers of “African biomes matter”.

Notably, some of the more recent studies focused on African gut microbiome (including of the Hadza in Tanzania) have been led by scientists from the global North. Disturbingly, some of these publications have often reported results about African subjects without including contributions from African scientists.

While collaborations with scholars from across the globe will be essential, the writers emphasise that the work must be led by Africans. “This will ensure that the research is sustainable, sufficiently acknowledges indigenous knowledge and communities and results in improved human capacity on the continent.”