Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their
functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the
kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions.
Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture
(KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community
comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the
KMC under different conditions revealed the core part of the community which included acetobacteria of two genera
Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among
which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas
spp., which previously had not been described in KMC, were found to be minor but permanent members of
the community. The community composition was dependent on the growth conditions. The bacterial component of
KMC was relatively stable, but may include additional member—lactobacilli. The yeast species composition was significantly
variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality
of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental
bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink.
As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community
composition should be provided by using DNA metabarcoding.