Functional Potential of Microbial Communities in Traditional African Fermented Dairy products: a Metagenomic Study

Abstract

Background Africa is home to several indigenous dairy products that span across 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. Gaining insights into their fermentation microbiome is critical for improving product quality, upholding consumer 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 qiime2 pipeline and its plugins, DADA2 and phylogeny. Here, we decided to go a step further by conducting functional inference into the fermentation microbiome using the 16S rRNA dataset, which was generated after sequencing the V4 region of the bacterial community of the five dairy products. The functional inference was conducted using PICRUSt version 2. Results The study observed that the microbial composition of the dairy products primarily consists of an average of 12 phyla across the five dairy products: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Fusobacteria, Desulfobacterota, Deinococcota, Deferribacterota, Euryarchaetota, Spirochaetota, and Acidobacteriota. At the genus level, LAB, Lactobacillus, and Streptococcus dominate in Nono, Wara, and Nunu at (57.7%, n = 41176), (33.5%, n = 26689), and (39.3%, n = 30203) for the former and (16.6%, n = 11837), (36.7%, n = 29245) and (39.5%, n = 30324) for the latter. The functional analysis reveals an enriched functional potential of the five dairy products, converging and diverging of taxa contributions across the products. Conclusion All products reveal shared enrichment in core metabolic functions, particularly those related to ABC transporters, amino acid metabolism, sugar utilization, and biosynthetic pathways. Streptococcus dominated in the purine-rich environments of Nono and Nunu; Wara displayed LAB co-dominance with a focus on peptidoglycan metabolism; Kwerionik exhibited a 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. Collectively, these findings position traditional dairy fermentations as microbial ecosystems in dynamic, resilient, and deeply intertwined with indigenous knowledge.