Exploratory Amplicon-Based Metagenomic Profiling and Chemical Fingerprinting of Three Spontaneously Fermented Southern African Traditional Products

Traditional fermented foods are integral to African culinary heritage and nutrition, yet their microbial ecology remains underexplored in many regions. This study employed amplicon sequencing (16S rRNA and ITS) and Fourier Transform Infrared (FTIR) spectroscopy to characterize the microbial communities and biochemical profiles of spontaneously fermented cow’s milk (amasi), sorghum–maize slurry (ting-type gruel), and sour maize gruel (mahewu). Amasi displayed the highest diversity, dominated by Lactococcus and Malassezia restricta. Mahewu was dominated by Clostridium sensu stricto and Malassezia restricta. The ting-variant showed low diversity with Weissella dominance and Symbiotaphrina species. FTIR spectra corroborated these patterns, highlighting lipid/protein bands in amasi and carbohydrate/organic acid signatures in the fermented cereal products. Beta-diversity analyses confirmed strong substrate-driven separation, with limited shared taxa underscoring ecological specialization. These findings reveal how raw material composition and processing shape spontaneous fermentation outcomes, while highlighting potential safety risks from opportunistic taxa and opportunities for probiotic strain isolation from beneficial taxa. Future studies are required to determine the viability and characteristics of the microbial flora in these fermented beverages to determine if their occurrence is significant. The results in this study show that metagenomic and FT-IR spectroscopy can be used to profile traditional fermented products, but this must be coupled with in-depth metabolite analyses using quantitative instruments and machine learning technologies for predictive fingerprinting to determine the identity, safety, and functionality of these culturally significant foods.