Adaptations and Community Changes in Milk and Water Kefir Microbiomes in Response to Environmental Parameters as Revealed by the Kefir4All Project

Abstract Milk and water kefir are fermented beverages prepared by inoculating milk or sugar-rich solutions with kefir grains - containing complex microbial consortia of bacteria and yeast. The increasing global popularity of kefir has driven interest in their microbiomes. Beyond their culinary significance, kefir serves as a model system for studying microbial community assembly, ecological filtering, and evolutionary dynamics. Kefir’s suitability as a model is enhanced by its simplicity (including short fermentation times), adaptability to experimental manipulation, and scalability for both controlled laboratory studies and citizen science initiatives. In this study, we employed genome-resolved metagenomics to investigate milk and water kefir microbiomes, produced over 21 weeks from an initial common source milk or water kefir grain by citizen scientists, using diverse substrates and conditions. Early fermentation (weeks 1–9) was marked by rapid compositional, functional and volatile shifts, leading to reproducible transitions between community states, with values not changing considerably thereafter. At the strain level, we identified multiple coexisting strains within dominant species, with initial fluctuations. While rare environmental species occasionally appeared, they were selectively filtered and did not persist. The sustained coexistence of key species and strains, alongside the emergence of reproducible community types, highlights the resilience and stability of kefir microbiomes across both short- and long-term timeframes. Our findings reinforce kefir’s value as a model for investigating microbial interactions, environmental microbial acquisition, and strain-level dynamics. The co-occurrence patterns observed among specific strains and species provide insight into microbial assembly and persistence, with broader relevance to complex ecosystems such as the gut microbiome. By elucidating patterns of compositional and functional change and assessing how selective pressures shape microbial communities, this study underscores kefir’s utility in microbial ecology and evolution.