Dynamic microbiota in water kefir: microbial shift and ecological selection during fermentation

Abstract

This study provides a comprehensive analysis of the bacterial and fungal microbiota in four water kefir grain (WKG) samples of different geographical origins and their corresponding fermented beverages (WK), in order to understand microbial dynamics during fermentation. The findings reveal marked shifts in community composition and diversity, underscoring the selective and dynamic nature of the water kefir ecosystem.

WKG samples exhibited considerable microbial variability. Genera such as Clostridium, Ethanoligenens, Acetobacter, and Gluconacetobacter dominated specific grain samples. After fermentation, the microbial landscape became more homogeneous, with Liquorilactobacillus emerging as the dominant genus (43.9–65.2%) across all WK samples. Phylogenetic clustering indicated that even low-abundance taxa in grains, such as Lentilactobacillus, can proliferate under fermentation conditions, while others, such as Clostridium, were undetected post-fermentation—likely filtered by low pH, oxygen exposure, and antimicrobial metabolites produced by dominant yeasts and lactic acid bacteria.

Fungal diversity also decreased significantly. Grain samples displayed varying fungal profiles (e.g., Brettanomyces in WKG-A vs. Saccharomyces in WKG-MG), yet all fermented beverages were overwhelmingly dominated by Saccharomyces cerevisiae (97.5–100%). This dominance reflects Saccharomyces’ metabolic efficiency, acid and ethanol tolerance, and competitive exclusion of other yeasts such as Dekkera and Candida, which were initially present in grains.

Overall, the results highlight a transition from taxonomically diverse grain communities to fermentation-adapted microbiota dominated by specialized taxa. These findings emphasize the importance of microbial succession and ecological selection in determining water kefir composition and quality. They also offer valuable insights for optimizing artisanal and industrial production, balancing microbial control with the preservation of functional diversity to enhance product consistency and flavor complexity.

Supplementary Information: The online version contains supplementary material available at 10.1186/s12866-025-04461-y.

Keywords: Fermentation dynamics; Microbiota shift; Water kefir.

Fig. 1

The most abundant genera and their relative abundance in each water kefir grain samples (A) and water kefir beverage samples (B)

Fig. 2

Phylogenetic tree based on sequences of ASVs corresponding to clostridia bacteria present in grains The phylogenetic tree was constructed with 15 ASVs and type-strain sequences retrieved from NCBI reference database. The tree was constructed using the Maximum likelihood algorithm. Bootstrap values (1000 replicates) are indicated at the nodes

Fig. 3

Phylogenetic tree based on sequences of ASVs corresponding to lactic acid bacteria present in grains and beverages (A). Phylogenetic tree based on sequences of ASVs corresponding to acetic acid bacteria present in grains and beverages (B). The phylogenetic trees were constructed with 14 and 15 ASVs and type-strain sequences retrieved from NCBI reference database, respectively. The trees were constructed using the Maximum likelihood algorithm. Bootstrap values (1000 replicates) are indicated at the nodes

Fig. 4

The most abundant genera and their relative abundance in each water kefir grain samples (A) and water kefir beverage samples (B)

Fig. 5

Phylogenetic tree based on sequences of ASVs corresponding to yeasts present in grains and beverages. The phylogenetic tree was constructed with 28 ASVs and type-strain sequences retrieved from NCBI reference database. The tree was constructed using the Maximum likelihood algorithm. Bootstrap values (1000 replicates) are indicated at the nodes