Changes in gut microbiota composition following water kefir consumption in healthy adults

Fermented foods have gained increasing scientific interest for their potential to modulate gut microbiota and provide probiotic microorganisms with possible health benefits. This intervention trial examined the impact of daily consumption of water kefir, a sustainable plant-based fermented beverage, on gut microbiota composition in 40 healthy adults. Participants consumed 200 mL of homemade water kefir daily for 14 days, with fecal samples collected before and after the intervention. Some participants reported mild, transient gastrointestinal effects such as flatulence (32%) and bloating (24%), which are common when introducing live microorganisms, while others experienced reduced abdominal pain (28%), and most (66%) reported no noticeable change in symptoms. 16S rRNA sequencing revealed significant shifts in microbial composition, including a 6.5% decrease in Firmicutes and increases in Bacteroidetes (+ 21.6%) and Actinobacteria (+ 14.8%). At the species level, beneficial taxa such as Blautia spp. and Roseburia faecis increased, along with commensals including Bacteroides fragilis, Bacteroides uniformis, Gemmiger formicilis, Prevotella copri, and Parabacteroides distasonis (p < 0.01). Although α-diversity remained unchanged, β-diversity differed significantly between pre- and post-intervention samples (p = 0.025). By comparing the relative abundance of dominant genera in participants' gut microbiota and in water kefir, overlapping genera such as Lactobacillus, Bifidobacterium, Prevotella, Coprococcus, and Faecalibacterium were identified. Among these, Bifidobacterium and Prevotella increased, Coprococcus decreased, and Lactobacillus and Faecalibacterium remained stable. Genera exclusive to the gut microbiota also exhibited differential changes. These findings suggest that water kefir consumption is associated with modulation of the gut microbiota, including increases in saccharolytic and short-chain fatty acid (SCFA)-producing taxa, potentially influenced by its exopolysaccharides and microbial community. Some genera from water kefir may transiently affect the gut microbiome, and the concurrent increase in Bifidobacterium and Prevotella may suggest a potential probiotic-like effect. However, causality cannot be established, and further studies are needed to assess the persistence of these changes and their long-term clinical relevance.