Anna Y. Alekseeva

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 ~ 33 generations, at three rural farm sites. The microbial community composition was profiled through 16 S rDNA sequencing, and community-level functioning through volatile organic compounds, pH, and consistency. We observed a substrate-driven divergence of microbial communities, with low-fat milk enriched with Acetobacter , full-cream milk enriched with Lactococcus , and S26 enriched with Lactiplantibacillus and Leuconostoc . This pattern exhibited a temporal community succession but remained consistent between sites. Similarly, the community-level functionality diverged but remained largely repeatable to properties known for mabisi. Our findings suggest that novel environments drive a species sorting process in natural microbial communities, and this process persists over time. Additionally, the repeatability of its community-level functionality points to underlying functional redundancy within diverse and successive microbial communities. Our study not only advances the understanding of how microbial communities adapt 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.

Societal Impact Statement: Traditional fermented foods worldwide depend on naturally occurring microbes, yet the environmental sources shaping these microbes and their effects on food quality remain poorly understood. We investigated bacteria living inside the roots of wild plants used to produce Munkoyo, a widely consumed nonalcoholic fermented cereal beverage in Zambia, to determine how plant species and local growing conditions influence these microbial communities. We found that both plant species identity and soil environment shape the root microbes that seed fermentation. These findings can improve beverage quality, support the cultivation of threatened species, and promote sustainable access to ingredients, helping protect nutrition, livelihoods and cultural heritage. Summary: Plants interact with diverse soil microbes through their roots, and these bacterial communities play vital roles in plant health and nutrient acquisition. In some traditional foods, root microbiomes of specific wild plant species act as natural starter cultures for fermentation. Yet, it remains unclear how distinct these root bacterial communities are among plant species and how much variation reflects plant identity versus growing environment. This study examined three wild plant species used as inoculum for producing Munkoyo, a traditional, nonalcoholic fermented cereal beverage in Zambia. Root endosphere, rhizosphere and bulk soil samples were collected from five districts, and bacterial communities were characterised using 16S rRNA gene amplicon sequencing. Bulk soil bacterial communities varied strongly across field sites and were structured by soil physicochemical properties, whereas root endosphere microbiomes were more distinct and differed among plant species and locations. The findings contribute to a better understanding of the bacterial communities involved in traditional fermented beverage production. They highlight the importance of plant species and soil environment in structuring root microbiomes, with implications for fermentation quality, sustainable cultivation of fermentation plants, and cultural heritage preservation.

The human gut contains a complex and highly variable microbial ecosystem of which the composition is affected by the health condition, lifestyle and diet of the host. Fermented dairy products harbour microorganisms favourable to the human gut microbial community. Mabisi, a spontaneous fermented local dairy product from Zambia, carries a variety of potentially beneficial microorganisms. Using the gastrointestinal tract (GI-tract) model system, SHIME^®, we tested how the administration of mabisi affects the composition and functionality of the human colon gut microbiota. After ten days of feeding mabisi into the GI-tract model system, the composition of the gut microbial community shifted towards a more even distribution of genera was similar to the community composition obtained by intervention with a standard prebiotic, fructooligosaccharide (FOS). This effect remained even when mabisi was heat-treated and all bacteria there were killed prior to the administration. Comparably to FOS, the microbial shift after mabisi treatment coincides with an increase in concentration of short chain fatty acids. Our findings suggest that mabisi carries important bioactive compounds with a prebiotic potential and might support and stabilize the gut microbial community.

Natural (microbial) communities are complex ecosystems with many interactions and cross-dependencies. Among other factors, selection pressures from the environment are thought to drive the composition and functionality of microbial communities. Fermented foods, when processed using non-industrial methods, harbor such natural microbial communities. In non-alcoholic fermented foods the fermenting microbiota is commonly dominated by 4–10 species of bacteria, which make them suitable model systems to study ecosystem assembly and functioning. In this study, we assess the influence of the environment on the composition of microbial communities of traditional fermented products from Africa. We compare differences between microbial communities that are found in similar products but come from different countries, hypothesizing they experience different environmental selection pressures. We analyzed bacterial community composition in 36 samples of various cereal-based fermented foods from Benin, Tanzania and Zambia using 16S rDNA amplicon sequencing. The differential abundance analysis indicates that the bacterial communities of fermented foods from the three countries are dominated by mostly lactic acid bacteria belonging to the genera of Lactobacillus, Weisella and Curvibacter. The samples from Zambia contain the most dissimilar microbial communities in comparison with samples from Benin and Tanzania. We propose this is caused by the relatively low temperature in Zambia, suggesting that indeed environmental selection can shape community composition of fermenting microbes.