Characterizing microbiomes of African fermented foods in a global context
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Date
2026-05-05
Authors
Leech, J.
Obafemi, Y.D.
Breselge, S.
Aremu, T.
Obadina, A.O.
Itohan, M.E.
Ezekiel, C.N.
Parkouda, C.
Tankoano, A.
Traoré, K.
Journal Title
Journal ISSN
Volume Title
Publisher
Microbiology Society
Published Version
Abstract
Fermentation plays a vital role globally, shaping traditional diets and enhancing food preservation, nutrition and flavour. With over 5,000 varieties of fermented foods globally, the microbiomes of many of these have yet to be explored, particularly with respect to those produced in some regions of Africa. To begin to address this knowledge gap, we conducted a shotgun metagenomics-based analysis of 91 fermented foods produced in Burkina Faso, Ghana, Kenya and Nigeria and compared them to a larger, global curated Food Metagenomic Database (cFMD). As for other studies of fermented food microbiomes in general, the substrate that was fermented emerged as the primary determinant of microbial beta diversity within the current African dataset and between the broader cFMD dataset. However, it was notable that the newly studied samples showed a small but statistically significant geographic signal. The African samples also displayed more alpha diversity than the global dataset, with cassava-, seed- and grain-based samples having the highest alpha diversity among the African foods. We also characterized the functional and antimicrobial profiles of all food-derived metagenome-assembled genomes (MAGs), noting the prevalence of pathways associated with carbohydrate metabolism across both African and non-African MAGs and an absence of known antimicrobial resistance genes in numerous genera. These findings not only expand our fundamental understanding of Africa's under-studied fermented food microbiomes but also lay the foundation for starter culture development tailored to local substrates and conditions, fostering opportunities to enhance product safety, quality and scalability while retaining key characteristics associated with the original, artisanal product.
Description
Keywords
Africa , Antimicrobial resistance (AMR) , Bacteria , Bacterium , Beta diversity , Burkina Faso , Classification , Fermentation , Fermented Foods , Fermented foods , Food Microbiology , Food control , Genetics , Ghana , Isolation and purification , Kenya , Metabolism , Metagenome , Metagenome-assembled genomes (MAGs) , Metagenomics , Microbiology , Microbiota , Microflora , Virulence , [APCMicrobiome] , [Microbiology] , fermented product
Citation
Leech, J, Obafemi, Y D, Breselge, S, Aremu, T, Obadina, A O, Itohan, M E, Ezekiel, C N, Parkouda, C, Tankoano, A, Traoré, K, Banwo, K, Kunadu, AP-H, Madilo, F K, Sanni, A I, Ogunremi, O R, Onipede, G, Odeny, D A, Otieno, C, Claesson, M J & Cotter, P D 2026, 'Characterizing microbiomes of African fermented foods in a global context', Microbiology (Reading), vol. 172, no. 5, 001695. https://doi.org/10.1099/mic.0.001695