Characterizing microbiomes of African fermented foods in a global context

Simple item page
dc.contributor.authorLeech, J.
dc.contributor.authorObafemi, Y.D.
dc.contributor.authorBreselge, S.
dc.contributor.authorAremu, T.
dc.contributor.authorObadina, A.O.
dc.contributor.authorItohan, M.E.
dc.contributor.authorEzekiel, C.N.
dc.contributor.authorParkouda, C.
dc.contributor.authorTankoano, A.
dc.contributor.authorTraoré, K.
dc.contributor.authorBanwo, K.
dc.contributor.authorKunadu, A.P.-H.
dc.contributor.authorMadilo, F.K.
dc.contributor.authorSanni, A.I.
dc.contributor.authorOgunremi, O.R.
dc.contributor.authorOnipede, G.
dc.contributor.authorOdeny, D.A.
dc.contributor.authorOtieno, C.
dc.contributor.authorClaesson, M.J.
dc.contributor.authorCotter, P.D.
dc.contributor.funderHorizon 2020
dc.contributor.funderScience Foundation Ireland(SFI)
dc.date.accessioned2026-05-18T14:50:05Z
dc.date.available2026-05-18T14:50:05Z
dc.date.issued2026-05-05
dc.description.abstractFermentation 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.en
dc.description.sponsorshipThis work was supported by the MASTER EU Consortium, funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 818368, and by Science Foundation Ireland (SFI) under grant no. SFI/12/RC/2273 (APC Microbiome Ireland).
dc.description.versionPublished Version
dc.format.extent16
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid001695
dc.identifier.authororcidLeech, J.
dc.identifier.authororcidObafemi, Y.D.
dc.identifier.authororcidBreselge, S.
dc.identifier.authororcidAremu, T.
dc.identifier.authororcidObadina, A.O.
dc.identifier.authororcidItohan, M.E.
dc.identifier.authororcidEzekiel, C.N.
dc.identifier.authororcidParkouda, C.
dc.identifier.authororcidTankoano, A.
dc.identifier.authororcidTraoré, K.
dc.identifier.authororcidBanwo, K.
dc.identifier.authororcidKunadu, A.P.-H.
dc.identifier.authororcidMadilo, F.K.
dc.identifier.authororcidSanni, A.I.
dc.identifier.authororcidOgunremi, O.R.
dc.identifier.authororcidOnipede, G.
dc.identifier.authororcidOdeny, D.A.
dc.identifier.authororcidOtieno, C.
dc.identifier.authororcidClaesson, M.J.§0000-0002-5712-0623
dc.identifier.authororcidCotter, P.D.
dc.identifier.citationLeech, 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
dc.identifier.doi10.1099/mic.0.001695
dc.identifier.issn1465-2080
dc.identifier.issued5
dc.identifier.journaltitleMicrobiology (Reading)
dc.identifier.otherRIS: urn:67CD2DD491B2DC54C1B73674B9A62F50
dc.identifier.otherORCID: /0000-0002-5712-0623/work/215061856
dc.identifier.urihttps://hdl.handle.net/10468/18778
dc.identifier.volume172
dc.language.isoen
dc.publisherMicrobiology Society
dc.relation.urihttps://www.scopus.com/pages/publications/105038059571
dc.relation.urihttps://www.scopus.com/pages/publications/105038059571?origin=resultslist
dc.rights© 2026, The Authors. This is an open- access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
dc.rights.accessrightsopen access
dc.rights.licensenameAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.statusPeer reviewed
dc.subjectAfrica
dc.subjectAntimicrobial resistance (AMR)
dc.subjectBacteria
dc.subjectBacterium
dc.subjectBeta diversity
dc.subjectBurkina Faso
dc.subjectClassification
dc.subjectFermentation
dc.subjectFermented Foods
dc.subjectFermented foods
dc.subjectFood Microbiology
dc.subjectFood control
dc.subjectGenetics
dc.subjectGhana
dc.subjectIsolation and purification
dc.subjectKenya
dc.subjectMetabolism
dc.subjectMetagenome
dc.subjectMetagenome-assembled genomes (MAGs)
dc.subjectMetagenomics
dc.subjectMicrobiology
dc.subjectMicrobiota
dc.subjectMicroflora
dc.subjectVirulence
dc.subject[APCMicrobiome]
dc.subject[Microbiology]
dc.subjectfermented product
dc.titleCharacterizing microbiomes of African fermented foods in a global contexten
dc.typeArticle (peer-reviewed)
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
mic001695.pdf
Size:
3.45 MB
Format:
Adobe Portable Document Format
Download
Collections
School of Microbiology
APC Microbiome Ireland