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

de Mel, Rumathi LU orcid ; Al-Khafaji, Alia LU ; Muthusamy, Saraladevi LU ; Xu, Jie LU and Håkansson, Åsa LU orcid (2026) In Scientific Reports 16.
Abstract
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... (More)
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. (Less)
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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Water kefir, Fermentation, Plant-based alternatives, Probiotic potential, Gut health, Next generation sequencing (NGS), Diversity, Relative Abundance
in
Scientific Reports
volume
16
article number
16006
pages
14 pages
publisher
Nature Publishing Group
external identifiers
  • pmid:42174008
ISSN
2045-2322
DOI
10.1038/s41598-026-53645-7
language
English
LU publication?
yes
id
e240f7d5-24de-437d-8bfe-23a130882c33
date added to LUP
2026-05-25 13:43:48
date last changed
2026-05-26 10:17:14
@article{e240f7d5-24de-437d-8bfe-23a130882c33,
  abstract     = {{Fermented foods have gained increasing scientific interest for their <br>
potential to modulate gut microbiota and provide probiotic <br>
microorganisms with possible health benefits. This intervention trial <br>
examined the impact of daily consumption of water kefir, a sustainable <br>
plant-based fermented beverage, on gut microbiota composition in 40 <br>
healthy adults. Participants consumed 200 mL of homemade water kefir <br>
daily for 14 days, with fecal samples collected before and after the <br>
intervention. Some participants reported mild, transient <br>
gastrointestinal effects such as flatulence (32%) and bloating (24%), <br>
which are common when introducing live microorganisms, while others <br>
experienced reduced abdominal pain (28%), and most (66%) reported no <br>
noticeable change in symptoms. 16S rRNA sequencing revealed significant <br>
shifts in microbial composition, including a 6.5% decrease in Firmicutes<br>
 and increases in Bacteroidetes (+ 21.6%) and Actinobacteria (+ 14.8%). <br>
At the species level, beneficial taxa such as <i>Blautia</i> spp. and <i>Roseburia faecis</i> increased, along with commensals including <i>Bacteroides fragilis</i>, <i>Bacteroides uniformis</i>, <i>Gemmiger formicilis</i>, <i>Prevotella copri</i>, and <i>Parabacteroides distasonis</i> (<i>p</i> &lt; 0.01). Although <i>α-</i>diversity remained unchanged, <i>β</i>-diversity differed significantly between pre- and post-intervention samples (<i>p</i> = 0.025).<br>
 By comparing the relative abundance of dominant genera in participants’<br>
 gut microbiota and in water kefir, overlapping genera such as <i>Lactobacillus</i>, <i>Bifidobacterium</i>, <i>Prevotella</i>, <i>Coprococcus</i>, and <i>Faecalibacterium</i> were identified. Among these, <i>Bifidobacterium</i> and <i>Prevotella</i> increased, <i>Coprococcus</i> decreased, and <i>Lactobacillus</i> and <i>Faecalibacterium</i><br>
 remained stable. Genera exclusive to the gut microbiota also exhibited <br>
differential changes. These findings suggest that water kefir <br>
consumption is associated with modulation of the gut microbiota, <br>
including increases in saccharolytic and short-chain fatty acid <br>
(SCFA)-producing taxa, potentially influenced by its exopolysaccharides <br>
and microbial community. Some genera from water kefir may transiently <br>
affect the gut microbiome, and the concurrent increase in <i>Bifidobacterium</i> and <i>Prevotella</i><br>
 may suggest a potential probiotic-like effect. However, causality <br>
cannot be established, and further studies are needed to assess the <br>
persistence of these changes and their long-term clinical relevance.}},
  author       = {{de Mel, Rumathi and Al-Khafaji, Alia and Muthusamy, Saraladevi and Xu, Jie and Håkansson, Åsa}},
  issn         = {{2045-2322}},
  keywords     = {{Water kefir; Fermentation; Plant-based alternatives; Probiotic potential; Gut health; Next generation sequencing (NGS); Diversity; Relative Abundance}},
  language     = {{eng}},
  month        = {{05}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Scientific Reports}},
  title        = {{Changes in gut microbiota composition following water kefir consumption in healthy adults}},
  url          = {{http://dx.doi.org/10.1038/s41598-026-53645-7}},
  doi          = {{10.1038/s41598-026-53645-7}},
  volume       = {{16}},
  year         = {{2026}},
}