The study aims to elucidate how species sorting structure bacterial communities and their functionality following exposure to novel environments over time.
In microbial ecology, the response of microbial community diversity and function during extended exposure to novel environments remains poorly understood. We investigate this using microbial communities derived from mabisi, a traditional fermented milk product from Zambia, as a model system. We propagated a shared ancestral mabisi microbial community into varied substrates, including raw cow milk (control), low-fat milk, full cream milk, F100 and S26 infant formulas, representing novel environments for ~ 200 generations. Samples were collected between propagations for microbial community profiling through 16S rDNA sequencing, and for community-level functioning through proxy analysis of metabolic volatile organic compounds and pH. We observed a substrate-dependent divergence of microbial communities, which transitioned from Leuconostoc and Streptococcus-enriched communities during the short-term propagation phase (first ~20 generations) to a Lactiplantibacillus, Lacticaseibacillus, and Lactobacillus-enriched community over a longer-term propagation phase (up to ~ 200 generations). However, the overall community-level functionality was repeatable between substrates over propagation phases, although it occurred to varying magnitudes. Our findings suggest that the trajectory of microbial community diversity fluctuates between distinct ecological clusters, reminiscent to attaining alternative stable states upon exposure to environmental changes over time, yet their community-level functionality remains largely repeatable.