Ezekiel, C. N. | Search bioRxiv

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↗

bioRxiv2023

Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome

Early-life exposure to natural and synthetic chemicals can impact acute and chronic health conditions. Here, a suspect screening workflow anchored on high-resolution mass spectrometry was applied to elucidate xenobiotics in breast milk and matching stool samples collected from Nigerian mother-infant pairs (n = 11) at three time points. Potential correlations between xenobiotic exposure and the developing gut microbiome, as determined by 16S rRNA gene amplicon sequencing, were subsequently explored. Overall, 12,192 and 16,461 features were acquired in the breast milk and stool samples, respectively. Following quality control and suspect screening, 562 and 864 features remained, respectively, with 149 of these features present in both matrices. Taking advantage of 242 authentic reference standards measured for confirmatory purposes of food bio-actives and toxicants, 34 features in breast milk and 68 features in stool were identified and semi-quantified. Moreover, 51 and 78 features were annotated with spectral library matching, as well as 416 and 652 by in silico fragmentation tools in breast milk and stool, respectively. The analytical workflow proved its versatility to simultaneously determine a diverse panel of chemical classes including mycotoxins, endocrine-disrupting chemicals (EDCs), antibiotics, plasticizers, perfluorinated alkylated substances (PFAS), and pesticides although it was originally optimized for polyphenols. Spearman rank correlation of the identified features revealed significant correlations between chemicals of the same classification such as polyphenols. One-way ANOVA and differential abundance analysis of the data obtained from stool samples revealed that molecules of plant-based origin were elevated when complementary foods were introduced to the infants diets. Annotated compounds in the stool, such as tricetin, positively correlated with the genus Blautia. Moreover, vulgaxanthin negatively correlated with Escherichia-Shigella. Despite the limited sample size, this exploratory study provides high-quality exposure data of matched biospecimens obtained from mother-infant pairs in sub-Saharan Africa and shows potential correlations between the chemical exposome and the gut microbiome. Highlights- Suspect screening of exposure biomarkers in human breast milk and infant stool. - 542 features in breast milk and 864 in stool were identified or annotated. - Consumption of complementary foods influenced the chemical exposure of infants. - Correlations between xenobiotics in both biological matrices evaluated. - Dietary exposure correlated to the stool microbiome composition. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/566030v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@61ad1aorg.highwire.dtl.DTLVardef@ab99a5org.highwire.dtl.DTLVardef@1f44c17org.highwire.dtl.DTLVardef@1af8857_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗