Ezeh, C. F. | Search bioRxiv

bioRxiv2026

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

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.

microbiology↗

bioRxiv2025

Bacterial succession, functional organization, and ecological drivers during spontaneous ukwa (Treculia africana) fermentation

Spontaneous fermentation of ukwa (Treculia africana) involves complex microbial succession that remains poorly characterized. Here, bacterial community dynamics during ukwa fermentation were resolved across six time points using high-throughput 16S rRNA gene sequencing. Fermentation followed a structured, stage-wise trajectory, beginning with plant-associated aerobic taxa, transitioning through a mid-phase dominated by fermentative firmicutes, and culminating in late-stage enrichment of acid-tolerant lactic and acetic acid bacteria. Microbial richness increased progressively during fermentation, while community composition clustered by time and correlated strongly with declining pH and moisture. Multivariate analyses identified these physicochemical gradients as primary drivers of succession. Network analysis further revealed distinct co-occurrence modules, indicating coordinated microbial guilds that underpin functional transitions during fermentation. This study provides the first sequencing-based ecological framework for ukwa fermentation and highlights how environmental filtering and microbial interactions shape community assembly in traditional African solid-state fermentations. These insights provide a basis for improving process control and guiding future starter culture development for ukwa and related fermented foods.

microbiology↗