Water Kefir as a Model for Aggregative Development of Microbial Multicellularity within a Multispecies Biofilm

Abstract

Water kefir is a traditional fermented beverage and a non-dairy alternative to milk kefir. Water kefir grains are cauliflower-like aggregates, ranging in size from 1-20 mm. They are composed of an exopolysaccharide matrix derived from the fermentation substrate sucrose. The microbial community on and within the grains is a complex, highly stable multicellular aggregate typically consisting of 10-15 core species that primarily belong to three major groups: lactic acid bacteria, acetic acid bacteria, and yeasts. Remarkably, the structural organisation, stability, and growth of kefir grains cannot be readily explained by their constituent species alone, and attempts to reconstitute them from the isolated species have so far been unsuccessful. Here, we combined a comprehensive structural investigation of the macro- and micromorphology of water kefir grains with culture-dependent and -independent analyses of its microbial biodiversity. The dynamics and interactions within this complex microbial community were studied by combining flow cytometry, fluorescence-activated cell sorting, and amplicon sequencing of selected subpopulations. Furthermore, the growth of water kefir grains was spatiotemporally resolved and quantitatively characterised, thereby unravelling an emergent multicellular growth function, documented for the first time. Our combined evidence provides an unprecedented understanding of a highly structured and metabolically synergistic multicellular microbial aggregate and lets us propose water kefir as a model system for the aggregative development of microbial multicellularity from multiple species. It should lay the foundation for future mechanistic studies aimed at understanding how multispecies microbial communities self-organise into stable, spatially structured multicellular aggregates.