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Review

The Effects of Kefir on the Human Oral and Gut Microbiome

by
Eleni Grace Black
1,
Andrea Bugarcic
2,
Romy Lauche
2,
Emad El-Omar
1 and
Fatima El-Assaad
1,*
1
Microbiome Research Centre, School of Clinical Medicine, UNSW Medicine & Health, St George & Sutherland Clinical Campuses, Sydney, NSW 2217, Australia
2
National Centre for Naturopathic Medicine, Southern Cross University, Lismore, NSW 2480, Australia
*
Author to whom correspondence should be addressed.
Nutrients 2025, 17(24), 3861; https://doi.org/10.3390/nu17243861
Submission received: 4 November 2025 / Revised: 28 November 2025 / Accepted: 29 November 2025 / Published: 11 December 2025
(This article belongs to the Special Issue Anti-Inflammatory, Antioxidant, and Antimicrobial Potential of Natural Products)
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Abstract

Kefir, a fermented probiotic drink made from milk, water, or plant-based ingredients, has gained significant attention as a dietary supplement. Originating from the Caucasus Mountains over three thousand years ago, kefir is believed to harbor a range of health benefits through its ability to alter the composition of microbial niches within the human body. These microbial niches are called microbiomes and encompass the collective community of microbial organisms, their genomes and environment. The modern commercialization of kefir has driven the need for high-quality research into its impact on the human microbiome and associated health outcomes; however, there is currently very limited scientific evidence supporting effects of kefir consumption on the human oral and gut microbiome. High-quality human clinical trials are essential to establish the safety and effectiveness of kefir before it can be advised for use in treating conditions linked to the oral and gut microbiota or metabolic health. This literature review aims to critically analyze recent studies investigating the effect of kefir consumption on the oral and gut microbiome, as well as its potential implications for human health. By examining kefir’s effects on these interconnected microbial ecosystems, we can better understand its potential and limitations as a functional food for promoting systemic health.

1. Introduction

The term ‘microbiome’ was initially coined in 1988 by Whipps et al. to describe the symphony of microbes existing in soils [1]. Since then, the term has expanded to include assemblies of microorganisms critical in the maintenance of human health and describes both the living microorganisms within an ecological niche as well as their respective genomes. The human gut microbiome is largely considered the most critical microbiome given its influence on metabolic health, chronic diseases and immune health, as well as its intricate communication with distal organs and organ systems [2,3]. The gut microbiome is typically rich and vast, carrying approximately 100 trillion microbes that span across hundreds to thousands of species [4,5]. This is in stark contrast to the oral microbiome, another niche within the human body with great influence on human health. While over 700 bacterial taxa have been reported in the oral cavity, the precise number of microbes is only 50–100 billion, dwarfed by that of the gut [6]. Nevertheless, the oral microbiome remains a critical factor in influencing human health due to its role in digestive and metabolic functions as well as its wider link to systemic health [6]. Probiotics have been consumed across the globe for millennia and are believed to promote human health by altering the balance of microbiota within a specific niche. Most probiotic products act mainly on the gut, containing live microorganisms that compete with pathogenic bacteria for nutrients and adhesion sites by producing antimicrobial substances such as bacteriocins and organic acids [7,8,9]. Additionally, by interacting with the host’s immune system, these microbes can reduce local and systemic inflammation and support gut barrier integrity [10,11,12]. While probiotics are naturally present in foods like yogurt, sauerkraut (fermented cabbage), and kimchi (fermented mixed vegetables), they are also available as dietary supplements in capsule or powder form. The ability of probiotics to influence microbial niches in the human body makes them a valuable tool for promoting overall health and preventing disease [13,14].
Kefir is a probiotic milk beverage that originated in the Caucasus mountains over 3000 years ago [15]. It is produced using kefir grains, which are complex symbiotic communities of lactic acid bacteria, acetic acid bacteria and yeast embedded in a polysaccharide matrix. The grains are introduced to milk, typically cow, and initiate a fermentation process by which the milk becomes thickened and slightly sour. In commercial kefir production practices (Figure 1), milk is inoculated with kefir grains in a ratio of 1:30 to 1:50, and the mixture is then left to ferment for up to 24 h at room temperature [16,17]. Finally, the kefir grains are strained out, and the remaining liquid can be consumed immediately or stored at low temperatures for future consumption [17,18]. Kefir can also be made using goat and sheep milk, or from vegan alternatives such as soymilk and water [19,20]. As the commercial kefir market has expanded, so too have the options for low-lactose and vegan alternatives, thereby allowing individuals with specific dietary requirements to consume the beverage. However, the exact microbial composition of kefir beverages, and therefore the health benefits they confer, may largely depend on the liquid substrate used during fermentation [19].
Indeed, an important consideration in kefir research is the inherent heterogeneity of kefir itself. Kefir composition varies considerably depending on multiple factors, including the microbial profile of the starter grains, fermentation time, and fermentation temperature [21,22,23,24]. These production variables can significantly influence the final microbial species present in the beverage, their relative abundances, and the concentration of bioactive metabolites produced during fermentation. Consequently, the specific health effects observed in one study may not be directly comparable to those in another, as different kefir preparations may exert distinct effects on the oral microbiome. For this reason, evidence on changes in the gut and oral microbiome following kefir consumption can largely differ [25,26].
The microbial composition of kefir is largely dominated by lactic acid bacteria (LAB), representing 60–83% of the microbial population [27,28,29,30] (Figure 2). LAB play a crucial role in the fermentation of milk substrates by metabolizing lactose and producing lactic acid. During this process, LAB also produce carbon dioxide, acetaldehyde, bacteriocins, cathelicidin and hydrogen peroxide, which have been demonstrated to attenuate and/or eradicate common enteric pathogens [31,32]. Lentilactobacillus kefiri, Lactococcus lactis and Leuconostoc mesenteroides are among the most abundant LAB present in kefir [33,34]. L. kefiri and L. mesenteroides survive passage to the gut and adhere to the epithelial lining, a critical feature of potential probiotics [35,36]. In the gut, these species display antibacterial and antifungal properties [35,36,37]. L. kefiri has also been found to bind toxic metals and mycotoxins, boasting its potential for future use in emergency toxicology [38,39]. L. mesenteroides can produce linoleic acid, a compound with antiatherogenic, anti-inflammatory, and anticarcinogenic properties [36]. L. lactis, in comparison, can produce conjugated linoleic acid but is unable to adhere to intestinal epithelium to colonize the gut [40,41]. Despite its transient presence in the gut, L. lactis can confer benefits to the host by producing biological compounds with immunomodulatory, antibacterial and antihypertensive effects [41]. It is this characteristic of L. lactis that earned it the term ‘cell factory’, with several studies showing its potential as a vehicle to deliver therapeutics and vaccines [42,43,44,45,46]. Other LAB species present in kefir include Lactobacillus acidophilus, Lactobacillus delbrueckii, Lactobacillus helveticus, Lactobacillus johnsonii, Lentilactobacillus parakefiri, Lentilactobacillus sunkii, Lacticaseibacillus rhamnosus, Lacticaseibacillus casei, Lacticaseibacillus paracasei, Lactiplantibacillus plantarum, Levilactobacillus brevis, Limosilactobacillus fermentum, and Limosilactobacillus reuteri [47,48]. However, the proportion and even the presence of each bacterial species in kefir varies across regions, substrates used and manufacturers [47,49,50].
The remaining 17–40% of microbial load in kefir is largely distributed amongst acetic acid bacteria (AAB) and yeast [16,29,30,47]. AAB such as Acetobacter lovaniensis, Acetobacter fabarum, Acetobacter orientalis, Gluconobacter liquefaciens and Gluconobacter oxydans have been identified in kefir [51]. These bacteria play a role in the fermentation of kefir along with LAB, producing acetic acid, a key short-chain fatty acid (SCFA) in the gut [52,53,54]. Acetic acid and its metabolites have local effects, such as an increase in ileal motility and colonic blood flow, as well as maintenance of epithelial homeostasis [55,56,57]. Recent studies also highlight its influence on systemic health, through modulation of host inflammation, energy expenditure and appetite [57]. Yeasts present in kefir include both lactose-fermenting species, such as Kluyveromyces marxianus and Kluyveromyces lactis, and non-lactose fermenting species, such as Saccharomyces cerevisiae [30,58,59]. S. cerevisiae, K. marxianus and K. lactis produce ethanol and carbon dioxide, contributing to kefir’s distinct flavor and mild effervescence [60,61]. Yeasts present in kefir are generally safe and well-tolerated for human consumption; indeed, many yeasts are considered probiotics as they support immune function and gut health [62]. Specifically, S. cerevisiae var. boulardii exhibits antimicrobial, anticarcinogenic, antioxidant and anti-inflammatory properties [63] and has been documented to cure or prevent Crohn’s disease [64] and irritable bowel syndrome [65]. Evidence suggests that S. cerevisiae may also enhance the probiotic potential of LAB via coaggregation and adhesion to epithelial cells [66], which is a particularly notable finding when considering the overall microbial profile of kefir. Kefir also contains Bifidobacterium longum, belonging to the Bifidobacteriaceae family. While neither LAB nor AAB, this species is known to have probiotic characteristics [67,68].
The unique combination of these microbial components is believed to contribute to kefir’s diverse range of potential health benefits, including improved gut health and management of various diseases [28,33,48]. The increasing popularity of kefir worldwide warrants further research into the impact of its consumption on human health. This review explores the current evidence the effect of kefir consumption on the oral and gut microbiome, the implications for human health and identifies key areas for future research.

2. Methods

A search was conducted using PubMed and Cochrane Library covering the period from January 2010 to February 2025. Search terms included “kefir” AND (“gut microbiota” OR “gut microbiome” OR “oral microbiota” OR “oral microbiome” OR “salivary”). A total of 126 results were retrieved, and 9 studies were included [69,70,71,72,73,74,75,76,77].
Studies were included if they met the following criteria: (1) randomized controlled trials, interventional studies, or safety/feasibility studies; (2) initial publication between January 2010 and December 2024 (3) methods included identification of gut or oral microbiota via DNA extraction and sequencing or culturing methods; and (4) outcomes included changes in the diversity or relative abundance or count of gut or oral microbiota. Studies were excluded if they were non-human studies, reviews, meta-analyses, case reports, or studies not available in English. Studies on any type of kefir (cow, goat, soy, water, etc.) were eligible for inclusion. Most studies were excluded as they were not randomized controlled trials, interventional studies, or safety feasibility studies, and did not measure changes in the diversity or relative abundance or count of gut or oral microbiota.
One further study was identified in the references of another included study [78]. Four studies were included examining the impact of kefir consumption on the oral microbiome, and six were included for the gut microbiome [69,70,71,72,73,74,75,76,77,78].

3. Results

Six relevant studies examining the gut microbiome and four examining the oral microbiome were identified (Table 1 and Table 2).

4. Discussion

4.1. Changes in the Gut Microbiome Induced by Kefir Consumption

Kefir consumption induces variable changes in the gut microbiome across different populations. In healthy adults, Walsh et al. [72] found that a subset of individuals experienced an increase in relative abundance of Lactococcus raffinolactis, a LAB present in milk kefir products. This change was not statistically significant, and there was no evidence of changes in microbial diversity between the three groups included in the study. In comparison, Bellikci-Koyu et al. [73] observed a significant increase in the relative abundance of Actinobacteria in individuals with metabolic syndrome. Yılmaz et al. [74] reported an increased relative abundance of Lactobacillus in individuals with IBD. Among critically ill patients admitted to hospital, Gupta et al. [71] noted an increase in the Gut Microbiome Wellness Index (GMWI) despite decreases in diversity and richness of gut microbiota due to antibiotic use. In contrast, Dazıroğlu et al. [70] found a significant increase in gut microbial diversity and richness in female with PCOS following kefir consumption, possibly due to the exclusion of participants using antibiotics. This collective data indicates the impact of kefir consumption on the gut microbiome is highly dependent on host health and lifestyle factors.
Despite variation across studies, several common findings emerged. Three studies reported a link between increased LAB levels and improvements in health outcomes. Yılmaz et al. [74] observed an increase in Lactobacillus levels in individuals with IBD, correlating with improvements in gastrointestinal symptoms, particularly in the ‘abdominal pain’ and ‘feeling good’ scores. Similarly, Gupta et al. [71]. reported an increase in Lactobacillus as being linked to improved GMWI in critically ill adults. However, this increase was for a brief period of only 72 h during the study. Dazıroğlu et al. [70]. found a significant rise in Bacilli abundance in female with PCOS, as well as a statistically significant improvement in physical function and mental health scores compared to pre-treatment. Two studies provided some preliminary evidence that increased LAB could improve health, although clear links were not established. Walsh et al. [72] identified an increase in L. raffinolactis, though this was only in four of the ten participants in the kefir group. These four participants demonstrated increases in acetic acid, N, N-dimethylglycine and succinic acid in urine, metabolites which may support metabolism, muscle health and skin health [79,80,81]. However, specific changes in the health outcomes of these four participants were not reported. Bellikci-Koyu et al. [73] reported a minor increase in Lactobacillales in individuals with metabolic syndrome and positive changes in fasting insulin, TNF-a, IFN-y and blood pressure in the kefir group. However, changes in overall health outcomes were also not reported. This indicates that consumption of kefir, by initiating changes in the abundance of LAB in the gut microbiome, may lead to positive changes in gut health and systemic health. However, this was not reflected in the study by Öneş et al. [69]. However, it was found that minor improvements in athletic performance occurred following kefir consumption, though this was not statistically significant. These studies report associations rather than causal relationships, and there is little homogeneity between studies regarding improved health measures.
Among the reviewed studies, three studies reported using kefir from different manufacturers [69,71,72], two reported formulating their own kefir from different manufacturers [70,73], and one did not report the manufacturer of the kefir used [74]. Standardised sources would enable more reliable cross-study comparisons. The inclusion of placebo controls in study designs helps to ensure the validity of results, yet only one study compared the kefir intervention group with a control group receiving a placebo treatment [73]; two studies included a control group that received no treatment [69,74], and the remaining three studies did not include a control group [70,71,72]. Larger-scale trials are also needed, given the limited sample sizes across all included studies.

4.2. Changes in the Oral Microbiome Induced by Kefir Consumption

Across all studies, kefir consumption in humans appeared to reduce the abundance of specific oral microbiota. All four studies reported reduced colony-forming units (CFU) of salivary Streptococcus mutans, a key contributor to dental caries, following a period of kefir consumption [75,76,77,78]. Cogulu et al. [78] also reported reduced CFU of salivary Lactobacillus, which includes species that both contribute to and prevent dental caries. This finding was not reflected in the remaining three studies. However, the general response to kefir consumption appears consistent across age groups. Two studies focused on healthy adults, demonstrating reductions in cariogenic bacteria S. mutans [77,78]. The remaining two studies involved children undergoing orthodontic treatment or dental restorations and demonstrated the same reduction [75,76]. This suggests that regardless of age or dental health status, kefir consumption may reduce the prevalence of cariogenic bacteria. However, due to the limited outcomes and the lack of long-term follow-ups across all four studies, there is no evidence to confirm that kefir consumption directly reduces the risk of dental caries or other dental diseases via modulation of the oral microbiome. Further studies should include assessment of clinical outcomes via long-term follow-ups to further elucidate the link between kefir consumption and the support of overall oral health.
While reductions in salivary S. mutans and Lactobacillus were reported across the four studies, these were the only observed changes in the oral microbiome. This represents a critical limitation of the literature, as all four studies relied exclusively on culture-based methods to identify bacteria present in participant salivary samples. None of the four reported studies used DNA sequencing methods to identify bacteria; instead, culturing methods and Caries risk tests (CRT) were used [75,76,77,78]. CRT involves collecting patient saliva and using an in-built agar media to visually determine the abundance of S. mutans and Lactobacilli present in saliva. As these methods are semi-quantitative and only test for the presence of pre-determined bacteria, they cannot provide a comprehensive view of microbial diversity, nor can they identify non-predetermined and novel species; this can only be achieved via DNA sequencing methods. Thus, the sole reliance on culture-based identification methods across all four studies majorly precludes comprehensive assessment of kefir consumption’s broader effects on oral microbial ecology.
Other limitations of the four studies include the varied kefir product manufacturers. One study used kefir grains from an unidentified manufacturer to produce a kefir product given to participants [77], two studies used different sources [76,78], and one did not report on the manufacturer of the kefir used [75]. Another limitation is the relatively small cohorts; only two trials included over 50 participants [76,77], with one of these not reporting the participants’ allocations to respective groups [77]. Larger-scale trials are needed to ensure reliable results. Furthermore, there was no evidence across the four studies of strict control of confounding factors, such as participant oral hygiene and dietary habits. While Alp et al. [76] state that participants received oral hygiene education and were advised to brush twice daily, details regarding the nature and content of the education were not included, and participant compliance with recommended oral hygiene practices was not recorded. Similarly, Reddy et al. [75] directed participants to maintain their usual hygiene practices, yet there is no evidence to suggest that authors monitored compliance or adjusted for its potential effects. Finally, the two remaining studies did not specify any instructions regarding participants’ oral hygiene practices [77,78]. These studies also employed intervention periods of three weeks or less [77,78], a short intervention period relative to other studies on the gut and oral microbiome. This short period may not be sufficient to allow changes in the oral microbiome to occur following kefir consumption. The short intervention period therefore stands as a major limitation for these two studies.

5. Conclusions

The current literature indicates that kefir consumption may influence both the gut and oral microbiomes in humans, but the specific nature and magnitude of these effects differ. In the gut, kefir appears to influence the relative abundance of Lactobacillus, with some studies also showing improvements in wellness indices and clinical parameters. In the oral cavity, kefir consistently reduces levels of Streptococcus mutans, a primary contributor to dental caries; a result observed in both adult and child populations. However, the variations in study designs and outcome measures makes it difficult to draw definitive conclusions about the specific mechanisms and long-term clinical implications of kefir consumption.

6. Future Directions

Future research should aim to overcome the multiple limitations present in the current body of studies. Recurring issues such as small sample sizes, brief intervention periods, and the absence of appropriate controls undermine the translation of the data. Additionally, variations in kefir grain sources or kefir manufacturers across the studies may introduce confounding factors that influence study results. In oral microbiome studies, the reliance on culture-based methods and Caries risk tests, rather than next-generation sequencing, severely restricted the scope of research to changes in the count of pre-determined bacteria. As a result, changes in alpha or beta diversity and relative abundance were not assessed. Future research should address these gaps through larger, well-controlled trials with age-, sex-, and ethnicity-matched participants using standardized kefir products, well-described kefir bases (dairy vs. plant-based) and comprehensive microbiome profiling. Additionally, longitudinal studies are needed to evaluate kefir’s long-term impact on clinical outcomes, including dental caries incidence and gut-related disorder prevention or management. Addressing these limitations would provide a more comprehensive understanding of kefir’s health benefits and therapeutic potential.

Author Contributions

Conceptualization F.E.-A., methodology E.G.B. and F.E.-A., software, writing—original draft preparation, E.G.B.; writing—review and editing, E.G.B., A.B., R.L., E.E.-O., F.E.-A.; supervision, F.E.-A. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Data Availability Statement

Data is contained within the article. The original contributions presented in this study are included in the article. Further inquiries can be directed to the corresponding author.

Conflicts of Interest

The authors declare no conflicts of interest.

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Nutrients 17 03861 g001
Figure 1. A simplified flowchart demonstrating commercial kefir production. Kefir grains are added to a base, either milk, water or plant-based beverage, in a ratio of 1:30 to 1:50 and the mixture undergoes fermentation at room temperature. After 24 h, the grains are strained out, and the remaining beverage can be consumed immediately or stored for later consumption. Created in BioRender. El-Assaad, F. (2025).
Figure 1. A simplified flowchart demonstrating commercial kefir production. Kefir grains are added to a base, either milk, water or plant-based beverage, in a ratio of 1:30 to 1:50 and the mixture undergoes fermentation at room temperature. After 24 h, the grains are strained out, and the remaining beverage can be consumed immediately or stored for later consumption. Created in BioRender. El-Assaad, F. (2025).
Nutrients 17 03861 g001
Nutrients 17 03861 g002
Figure 2. Microbial composition of kefir: lactic acid bacteria (65–80%), yeast (10–30%), acetic acid bacteria (8–20%) and others (<5%). Created in BioRender. El-Assaad, F. (2025).
Figure 2. Microbial composition of kefir: lactic acid bacteria (65–80%), yeast (10–30%), acetic acid bacteria (8–20%) and others (<5%). Created in BioRender. El-Assaad, F. (2025).
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Table 1. Comparison of six studies investigating the effect of kefir consumption on gut microbiota in humans. Abbreviations: ns = not statistically significant as reported in identified study; GMWI = Gut Microbiome Wellness Index; T1 = timepoint 1; T2 = timepoint; PCOS = polycystic ovarian syndrome; LOS = length of stay; CD = Crohn’s disease; UC = ulcerative colitis; NR = not reported.
Table 1. Comparison of six studies investigating the effect of kefir consumption on gut microbiota in humans. Abbreviations: ns = not statistically significant as reported in identified study; GMWI = Gut Microbiome Wellness Index; T1 = timepoint 1; T2 = timepoint; PCOS = polycystic ovarian syndrome; LOS = length of stay; CD = Crohn’s disease; UC = ulcerative colitis; NR = not reported.
Reference, CountryParticipantsTreatmentsDosageTreatment DurationKefir Product and Substrate UsedSampling MethodsIdentification MethodsKey FindingsLimitations
Öneş et al., 2025 [69]
Turkey		Professional female soccer players
n (intervention) = 12
n (control) = 9
Age(intervention) = 24.42 ± 2.52 years
Age (control) = 22.14 ± 3.61 years
Gender (intervention) = 100% female
Gender (control) = 100% female		Intervention received kefir; control received nothing.200 mL once daily4 weeksAltınkılıç Lactose-free Kefir, cow’s milkExternal faecal sample processed using DiaRex stool senomic DNA extraction kitV3–V4 region of 16S rRNA↑ Microbial richness and diversity in intervention group only (ns)
↑ Finishing speed and VO2max (ns)
Minor changes in relative abundance in intervention group only (ns)		Short duration; small sample size; no placebo control; no wash-out period; no analysis of dose-dependent effects; specific population
Dazıroğlu et al., 2024 [70]
Turkey		Females with PCOS
n (intervention) = 17
Age (intervention) = 24.7  ±  5.44 years
Gender (intervention) = 100% female		Participants received kefir250 mL once daily8 weeksAuthors formulated their own kefir through traditional practices using grains from Danem, substrate unclearExternal faecal sample processed using DiaRex stool genomic DNA extraction kitV3-V4 region of 16S rRNA↓ IL-6
↑ Bacilli
↑ Lactococcus
↑ Holdemania		Small sample size; no placebo control; no wash-out period; no analysis of dose dependent effects
Gupta et al., 2024 [71]
USA		Critically ill males and females
n (intervention) = 54
n (microbiota analysis) = 13
Age (intervention) = 64.6 ± 15.3 years
Gender (intervention) = 39% female		Patients received kefir60 mL, followed by 120 mL after 12 h, then 240 mL dailyUntil discharge of patientLifeway Foods Kefir, whole cow’s milkExternal faecal sample processed using Qiagen DNeasy 96 PowerSoil pro QIAcube HT kitShotgun metagenomic sequencing↑ Lactobacillus plantarum, L. reuteri, and L. rhamnosus from T1 to T2
↑ GMWI scores in critically ill adults.
↓ Shannon diversity and species richness
Administration was safe and feasible		Small sample size; no placebo control; no wash-out period; no analysis of dose-dependent effects; duration of intervention limited by LOS and death; high rate of antibiotic use
Walsh et al., 2023 [72]
Ireland		Healthy individuals
n (inulin) = 10
n (probiotic) = 10
n (kefir) = 9
Age (inulin) = NR
Age (probiotic) = NR
Age (kefir) = NR
Gender (inulin) = NR
Gender (probiotic) = NR
Gender (kefir) = NR		Inulin group received inulin; kefir group received kefir; probiotic group received probiotic247 mL once daily4 weeksNourish Kefir, substrate unclearExternal faecal sample processed using Qiagen QIAamp DNA stool mini kitShotgun metagenomic sequencing↑ Lactococcus raffinolactis in kefir group only (ns)Short duration; small sample size; no placebo control; no wash-out period; no analysis of dose-dependent effects
Bellikci-Koyu et al., 2019 [73]
Turkey		Males and females with metabolic syndrome
n (intervention) = 12
n (control) = 10
Age (intervention) = 52 (range 47.5–60.5)
Age (control) = 53 (range 45–60)
Gender (intervention) = 83% female
Gender (control) = 60% female		Intervention received kefir; control received unfermented milk180 mL once daily12 weeksAuthors formulated their own kefir using grains from Danisco, full-fat whole cow’s milkExternal faecal sample processed using Qiagen QIAamp DNA stool mini kitV3-V4 region of 16S rRNA↑ Actinobacteria;
↑ Lactobacillales (ns)
Positive changes in fasting insulin, TNF-a, IFN-y and blood pressure in kefir group (ns between groups)		Small sample size; no wash-out period; no analysis of dose-dependent effects; dietary confounding; no mechanistic explanation for changes in biological parameters studied
Yılmaz et al., 2019 [74]
Turkey		Individuals with IBD
n (intervention, CD) = 10
n (intervention, UC) = 15
n (control, CD) = 10
n (control, UC) = 10
Age (intervention, CD) = 33 (range 24–65)
Age (intervention, UC) = 33 (range 19–68)
Age (control, CD) = 42 (range 21–66)
Age (control, UC) = 43.5 (range 29–76) Gender (intervention, CD) = 60% female
Gender (intervention, UC) = 40% female
Gender (control, CD) = 40% female
Gender (control, UC) = 60% female		Intervention groups received kefir; control received nothing.400 mL twice daily4 weeksNR, substrate unclearExternal faecal sample processed using Qiagen QIAamp DNA stool mini kitQuantitative polymerase chain reaction and Sanger sequencing↑ Lactobacillus (CD/UC patients in kefir group only)Short duration; small sample size; no placebo control; no wash-out period; no analysis of dose-dependent effects; analysis limited to Lactobacillus; statistically significant differences in levels of faecal Lactobacillus between UC control and UC treatment groups at baseline
↑: increased; ↓: decreased.
Table 2. Comparison of six studies investigating the effect of kefir consumption on oral microbiota in humans. Abbreviations: NR = not reported; CFU = colony forming units.
Table 2. Comparison of six studies investigating the effect of kefir consumption on oral microbiota in humans. Abbreviations: NR = not reported; CFU = colony forming units.
Reference, CountryParticipantsTreatmentsDosageTreatment DurationKefir Product and Substrate UsedSampling MethodsIdentification MethodsKey FindingsLimitations
Reddy et al., 2021 [75]
India		Children with carious lesions post-restoration
n = 80
n (kefir) = NR
n (probiotic curd) = NR
n (probiotic drink) = NR
n (control) = NR
Age (kefir) = NR
Age (probiotic curd) = NR
Age (probiotic drink) = NR
Age (control) = NR
Gender (kefir) = NR
Gender (probiotic curd) = NR
Gender (probiotic drink) = NR
Gender (control) = NR		Kefir group received kefir; probiotic curd group received probiotic curd; probiotic drink group received probiotic drinks; control group received nothing.100 mL once daily4 weeksNR, substrate unclearUnstimulated saliva sampleCulture-based identification↓ Salivary Streptococcus mutans in kefir compared to the control group at 4 weeks.Group allocation NR; no wash-out period; limited outcome measures; no analysis of dose-dependent effects; dietary and behavioural confounding; control group had higher CFU Streptococcus mutans at baseline.
Alp et al.,
2018 [76]
Turkey		Children undergoing orthodontic treatment
n (kefir) = 15
n (probiotic toothpaste) = 15
n (control) = 15
Age (kefir) = 14.3 ± 1.7 years
Age (probiotic toothpaste) = 14.9 ± 2.0 years
Age (control) = 14.1 ± 2.1 years
Gender (kefir) = 47% female
Gender (probiotic toothpaste) = 67% female
Gender (control) = 67% female		Kefir group received kefir; probiotic toothpaste group brushed with probiotic toothpaste; control group brushed with regular toothpaste100 mL twice daily6 weeksAtatürk Orman Çiftliği (Atatürk Forest Farm) Kefir, substrate unclearStimulated saliva samplesCaries risk test↓ Salivary Streptococcus mutans in kefir and probiotic toothpaste groups compared to control at 3 weeks and 6 weeks.Short duration; small sample size; no wash-out period; limited outcome measures; no analysis of dose-dependent effects; dietary and behavioural confounding.
Ghasempour et al., 2014 [77]
Iran		Healthy individuals
n = 22
n (Group A) = 11
n (Group B) = 11
Age (Group A) = NR
Age (Group B) = NR
Gender (Group A) = NR
Gender (Group B) = NR		Crossover design. Participants in group A received kefir for two weeks, then 0.05% sodium fluoride for two weeks. Participants in group B received the same treatments in a reverse-parallel manner.100 mL once daily2 weeksAuthors formulated their own kefir, although did not specify manufacturer of grains used, cow’s milk.Unstimulated saliva sampleCulture-based identification↓ Salivary Streptococcus mutans in intervention and control compared with baseline after 2 weeks. Equal inhibitory effect was found between study groups.Short duration; small sample size; no analysis of baseline characteristics; limited outcome measures; no analysis of dose-dependent effects; dietary confounding.
Cogulu et al., 2010 [78]
Turkey		Healthy individuals
n (intervention, single dose) = 35
n (intervention, double dose) = 35
n (control) = 34
Age (intervention single dose) = NR
Age (intervention double dose) = NR
Age (control) = NR
Gender (intervention single dose) = NR
Gender (intervention double dose) = NR
Gender (control) = NR		Single dose group received kefir; double dose received twice the amount of kefir twice daily for 3 weeks; control group received 100 mL milk once daily for 3 weeks.100 mL; once daily for single-dose, twice daily for double-dose3 weeksSakipaga Kefir, substrate unclearStimulated saliva samplesCaries risk test↓ Salivary Streptococcus mutans in double-dose compared to single-dose and control after 3 weeks.
↓ Salivary Lactobacillus in double-dose compared to single-dose and control after 3 weeks.		Short duration; no wash-out period; limited outcome measures; dietary and behavioural confounding.
↓: decreased.
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Black, E.G.; Bugarcic, A.; Lauche, R.; El-Omar, E.; El-Assaad, F. The Effects of Kefir on the Human Oral and Gut Microbiome. Nutrients 2025, 17, 3861. https://doi.org/10.3390/nu17243861

AMA Style

Black EG, Bugarcic A, Lauche R, El-Omar E, El-Assaad F. The Effects of Kefir on the Human Oral and Gut Microbiome. Nutrients. 2025; 17(24):3861. https://doi.org/10.3390/nu17243861

Chicago/Turabian Style

Black, Eleni Grace, Andrea Bugarcic, Romy Lauche, Emad El-Omar, and Fatima El-Assaad. 2025. "The Effects of Kefir on the Human Oral and Gut Microbiome" Nutrients 17, no. 24: 3861. https://doi.org/10.3390/nu17243861

APA Style

Black, E. G., Bugarcic, A., Lauche, R., El-Omar, E., & El-Assaad, F. (2025). The Effects of Kefir on the Human Oral and Gut Microbiome. Nutrients, 17(24), 3861. https://doi.org/10.3390/nu17243861

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