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bioRxiv · 10.64898/2026.09.26.754590

Genome-Resolved Characterization of Stage-Associated Microbial Composition and Functional Potential During Spontaneous Ugba Fermentation

DIKE, K.·Ojukwu, C. C.·Oladele, F. T.·Ezeh, C. F.·Nwachukwu, M. I.
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Abstract

Ugba, a traditional alkaline-fermented condiment produced from African oil bean seeds (Pentaclethra macrophylla Benth.), remains poorly characterised at genome resolution. This study characterised a single spontaneous ugba fermentation using genome-resolved shotgun metagenomics across Early (0-24 h), Mid (48-96 h), and Late (120-144 h) composite stages. Thirty metagenome-assembled genomes (MAGs) were recovered and grouped according to their temporal abundance patterns. The Early-stage retained MAG population was dominated by Bacteroidota-associated MAGs, which exhibited the highest carbohydrate-active enzyme density and broad glycoside hydrolase repertoires, consistent with substantial genome-encoded potential for utilisation of the plant-derived seed matrix. The Mid stage showed marked restructuring of MAG composition, while Core and Late-associated MAGs increased towards fermentation maturation. Functional differentiation was also evident among Corynebacterium MAGs: C. nuruki encoded a complete urease system, whereas C. phoceense_A encoded glutamate dehydrogenase and nitrate-reduction genes. These stage-associated changes coincided with progressive alkalinisation from pH 7.15 to 8.01. Together, the results show that temporal restructuring of reconstructed microbial populations was accompanied by differentiation in genome-encoded functional potential. This study provides a genome-resolved characterisation of microbial composition and functional potential during spontaneous ugba fermentation and expands current understanding of the microbial organisation of this traditional African fermented food.

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DIKE, K., Ojukwu, C. C., Oladele, F. T., Ezeh, C. F., Nwachukwu, M. I.. 2026-09-26. Genome-Resolved Characterization of Stage-Associated Microbial Composition and Functional Potential During Spontaneous Ugba Fermentation. https://doi.org/10.64898/2026.09.26.754590

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