Daily consumption of 200 mL of homemade water kefir for 14 days was associated with significant shifts in gut microbiota composition in healthy adults, including increases in Bacteroidetes and Actinobacteria, changes in specific beneficial taxa, and significant β-diversity differences, though α-diversity remained unchanged.
Key Findings
Results
Water kefir consumption was associated with significant phylum-level shifts in gut microbiota, including decreases in Firmicutes and increases in Bacteroidetes and Actinobacteria.
Participants consumed 200 mL of homemade water kefir daily for 14 days (n=40 healthy adults)
Firmicutes decreased by 6.5% following the intervention
Bacteroidetes increased by 21.6% following the intervention
Actinobacteria increased by 14.8% following the intervention
16S rRNA sequencing was used to assess microbial composition from fecal samples collected before and after the intervention
Results
Several beneficial and commensal bacterial taxa at the species level increased significantly following water kefir consumption.
Blautia spp. and Roseburia faecis increased following the intervention
Commensals including Bacteroides fragilis, Bacteroides uniformis, Gemmiger formicilis, Prevotella copri, and Parabacteroides distasonis also increased
These species-level changes were statistically significant (p < 0.01)
These taxa include saccharolytic and short-chain fatty acid (SCFA)-producing bacteria
Results
β-diversity differed significantly between pre- and post-intervention samples, while α-diversity remained unchanged.
β-diversity difference between pre- and post-intervention samples was statistically significant (p = 0.025)
α-diversity showed no significant change following the intervention
Fecal samples were collected before and after the 14-day intervention period
Results
Overlapping genera found in both water kefir and participants' gut microbiota showed differential changes following the intervention.
Overlapping genera identified between water kefir and gut microbiota included Lactobacillus, Bifidobacterium, Prevotella, Coprococcus, and Faecalibacterium
Bifidobacterium and Prevotella increased following consumption
Coprococcus decreased following consumption
Lactobacillus and Faecalibacterium remained stable
Genera exclusive to the gut microbiota also exhibited differential changes
Results
Most participants reported no noticeable change in gastrointestinal symptoms, though mild transient effects were observed in a subset.
66% of participants reported no noticeable change in gastrointestinal symptoms
32% reported mild, transient flatulence
24% reported bloating
28% reported reduced abdominal pain
These gastrointestinal effects are described as 'common when introducing live microorganisms'
Discussion
The concurrent increase in Bifidobacterium and Prevotella following water kefir consumption may suggest a potential probiotic-like effect.
The authors note this may be 'potentially influenced by its exopolysaccharides and microbial community'
Some genera from water kefir may 'transiently affect the gut microbiome'
The authors caution that causality cannot be established from this study design
Further studies are needed to assess the persistence of these changes and their long-term clinical relevance
What This Means
This research suggests that drinking a small daily amount (200 mL, roughly a cup) of water kefir — a fermented, plant-based beverage made with water, sugar, and kefir grains — for just two weeks can meaningfully shift the types of bacteria living in the gut. In a study of 40 healthy adults, researchers found significant changes in the overall community structure of gut bacteria, with increases in groups like Bacteroidetes and Actinobacteria and a decrease in Firmicutes. Several specific bacterial species associated with gut health and the production of beneficial compounds called short-chain fatty acids also increased. Most participants (66%) experienced no negative symptoms, while smaller portions reported temporary and mild issues like gas or bloating, which are typical when consuming live microorganisms.
The study also compared which bacterial groups are naturally found in water kefir versus in the human gut. Some genera present in both — like Bifidobacterium and Prevotella, which are often associated with digestive health — increased after participants drank the kefir, hinting that bacteria from the beverage may have temporarily interacted with or supported existing gut communities. The overall diversity of species in participants' guts (how many different types were present) did not change, but the composition — which bacteria were more or less abundant — did shift detectably.
This research suggests that regular, short-term water kefir consumption can alter gut bacterial communities in potentially beneficial ways, but the authors are careful to note that this study cannot prove that these changes cause any specific health outcomes. It is not known how long these microbiota shifts last after stopping consumption, and larger and longer studies are needed to understand whether these changes have meaningful effects on health. Water kefir may be a sustainable and accessible way to influence gut microbiota, but further research is needed before drawing firm conclusions about its clinical benefits.
de Mel R, Al Khafaji A, Muthusamy S, Xu J, Håkansson &. (2026). Changes in gut microbiota composition following water kefir consumption in healthy adults.. Scientific reports. https://doi.org/10.1038/s41598-026-53645-7