Inferred functional potential of microbial communities in traditional African fermented dairy products using 16S rRNA

Background. Africa is home to several indigenous dairy products that span the continent. These dairy products are widely consumed and cherished for their rich nutritional profile and distinctive taste, shaped by microbial fermentation. However, their microbiome remains largely unexplored, thus limiting knowledge of microbial composition, diversity and functional inference. These limitations have implications for product quality and safety and scientific documentation. Methods. The 16S rRNA dataset on five popularly consumed dairy products, Nono, Wara, Kwerionik, Ghee and Nunu, with the SRA accession number PRJNA532858, was collected for taxonomic classification and diversity analysis using the Quantitative Insights into Microbial Ecology 2 pipeline. Functional inference was conducted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 version 2. Results. In this dataset, an average of 12 phyla were observed, including Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. At the genus level, lactic acid bacteria, particularly Lactobacillus and Streptococcus, were predominant in Nono, Wara and Nunu, with relative abundances: 57.7, 33.5 and 39.3% for Lactobacillus and 16.6, 36.7 and 39.5% for Streptococcus. Functional predictions revealed both shared and product-specific metabolic capabilities, with varying taxonomic contributions to key pathways across samples. Conclusion. Across the analysed samples, the products exhibit both conserved and distinct predicted functional signatures inferred from the 16S rRNA gene data. Particularly, those related to ATP-binding cassette transporters, amino acid metabolism, sugar utilization and biosynthetic pathways. Streptococcus dominated in the purine-rich environments of Nono and Nunu; Wara displayed lactic acid bacteria co-dominance, with a focus on peptidoglycan metabolism; Kwerionik exhibited broader microbial diversity, with a three-way taxonomic distribution; and Ghee stood out with Acetobacter-driven lipid and oxidative metabolism, showcasing the community's adaptive plasticity to distinct environmental and processing conditions. These findings suggest that traditional dairy fermentations function as complex microbial ecosystems and highlight their potential importance in food systems and microbial ecology.