Species sorting shapes the divergence of a traditional fermented dairy-derived bacterial community with repeatable functionality during propagation with alternative substrates

Species sorting underlies changes in microbial community composition under varying environments, yet predicting the species diversity and their functional outcomes when exposed to novel conditions remains challenging. We explored this using mabisi, a Zambian traditional fermented milk, by propagating a shared starting mabisi microbial community across five novel substrates - raw bovine milk (control), low-fat milk, full-cream milk, and the infant formulas F100 and S26 – under static conditions and fixed dilution for ~ 66 generations, at three rural farm sites. The microbial community composition was profiled through 16S rDNA sequencing, and community-level functioning through volatile organic compounds, pH, and consistency. We observed a substrate-driven divergence of microbial communities, with early-phase (~ 20 generations) communities enriched with Lactococcus , and transitioning to late-phase (~ 66 generations) communities enriched with Acetobacter , Lactiplantibacillus , Paucilactobacillus , Leuconostoc , Lacticaseibacillus , and Lactobacillus . This succession pattern remained consistent between sites. Despite community diversity shifts, community-level functionality remained largely repeatable. Our findings suggest that novel environments drive a species sorting process in natural microbial communities, and this process persists over time. Additionally, the maintenance of its community-level functionality despite community turnover points to underlying functional redundancy within diverse and successive microbial communities. Our study not only advances the understanding of how microbial community adapts to environmental changes but also provides a basis for harnessing the mabisi-derived microbial community for broad biotechnological applications, particularly supporting the feasibility and effectiveness of its use in an in-house formulated F100 infant formula for treating malnourished children in developing regions.