Comparative Profiling of Yeast Communities in Kefir Grains and Liquid Kefir Using ITS Amplicon Next-Generation...

Kefir is a fermented dairy beverage produced by a complex microbial consortium of bacteria and yeasts coexisting within a polysaccharide-protein matrix known as kefir grains. Although the bacterial communities are well-characterized, the distribution of yeast taxa, specifically those transitioning into the fermented liquid phase, remains insufficiently described. This study is aimed at characterizing and comparing the fungal community composition in both the kefir grains and the resulting fermented liquid. Using internal transcribed spacer (ITS) amplicon sequencing on samples from a traditionally propagated culture, we identified 122 yeast taxa in the grains and 221 taxa in the liquid fraction, with 182 taxa shared between both habitats. Crucially, taxonomic profiling of the liquid phase revealed a high diversity of yeasts, with Saccharomyces cerevisiae, Kluyveromyces marxianus, and Pichia kudriavzevii being significantly more abundant compared with the grain matrix. In contrast, grain samples were relatively enriched in Pichia fermentans. Several taxa maintained moderate abundance across both fractions, suggesting ecological persistence during fermentation. These patterns reflect the spatial distribution of yeast taxa within the system rather than functional specialization. Although based on a single culture without biological replication, these findings provide a detailed descriptive map of the kefir mycobiome, distinguishing dominant fermentation-associated yeasts in the liquid phase from low-abundance environmental fungi.