Kefir: the science of live fermentation for gut microbiota, digestion and metabolism

Kefir is a fermented drink produced by the symbiotic action of lactic acid bacteria, acetic acid bacteria and yeast present in kefir grains. It can be made with milk or sugared water, though most human clinical studies have looked at milk kefir.

More than a probiotic drink, kefir is a living food matrix. During fermentation, its microorganisms transform the substrate into a food rich in metabolites and bioactive compounds, such as organic acids, peptides, exopolysaccharides (including kefiran), vitamins and minerals. This combination helps explain the growing scientific interest in its role in gut microbiota, digestive function and metabolic markers.

As part of a health-promotion strategy, kefir is also a practical choice for favoring minimally processed foods and reducing sweetened drinks, sugary dairy desserts and ultra-processed foods in daily life. The human clinical literature already describes favorable effects on gut microbiota, gastrointestinal symptoms and some metabolic parameters, while experimental studies dig deeper into mechanisms related to the gut barrier, inflammation and oxidative stress.

Step-by-step: homemade kefir

Milk kefir

Ingredients

• 1 tablespoon of kefir grains
• 200 to 300 mL of pasteurized milk (whole or reduced-fat)
• A clean glass jar, a non-metallic sieve, and a cloth or breathable lid

How to make it

1. Put the grains in the glass jar (~1 heaping tablespoon) and add the cold milk.

2. Cover with a cloth or lid without sealing it completely, to let gases escape.

3. Let it ferment at room temperature, away from sunlight, for 12 to 24 hours. The longer it sits, the more tart it gets.

4. Strain with a non-metallic sieve, separating the grains from the liquid.

5. The kefir is ready to drink. Reuse the grains right away in fresh milk, or store them refrigerated for short breaks or frozen for longer ones.

Hygiene is essential. Utensils and hands need to be clean. Signs like mold, a strong unpleasant smell, a change in color, or an odd texture mean the batch should be discarded. Don’t over-extend fermentation - overly tart kefir loses palatability and increases the chance of biogenic amines.

Who can drink it, and who should be cautious or avoid it

Clinical evidence and microbiota modulation

Researchers (2025) ran a randomized clinical trial with healthy young adults in South Korea, comparing 150 mL/day of kefir, unfermented milk or yogurt for two weeks in a controlled dietary setting. Using long-read 16S rRNA sequencing (PacBio), the kefir group showed:

• An increase in lactate- and SCFA-producing bacteria, including Bifidobacterium breve, Ruthenibacterium lactatiformans, Weissella koreensis and Leuconostoc mesenteroides
• A significant increase in Blautia luti, a genus associated with SCFA production
• Enrichment of the SCFA-production functional pathway by predictive metagenomic analysis
• A subjective improvement in abdominal symptoms and bowel function in ~50% of participants

Researchers (2026) evaluated 250 mL/day of lactose-free kefir for six weeks in 65 healthy young adults. The main findings were:

• A significant reduction in gastrointestinal symptoms (GSRS scale), especially diarrhea scores
• A drop in total cholesterol, creatinine and serum uric acid
• A favorable trend in sleep quality, mental well-being, blood glucose and CRP

In parallel, Researchers (2025) reviewed the clinical literature between 2010 and 2025 on kefir and the oral and gut microbiome. The findings frame kefir as a functional food integrated into a healthy dietary pattern, with consistent benefits when incorporated into routine.

In summary, kefir modulates the gut microbiota, improves gastrointestinal symptoms, and contributes to lipid profile in healthy adults.

Bioactive compounds and potential mechanisms

Fermentation by lactic acid bacteria, acetic acid bacteria and yeast generates a complex bioactive matrix, which can include:

• Lactic acid bacteria (Lentilactobacillus kefiri, Lactococcus lactis, Leuconostoc mesenteroides, among others): they take part in lactose fermentation, lactic acid production and antimicrobial compounds, contributing to lower pH, competition with pathogenic microorganisms, and gut microbiota modulation.
• Yeast (Kluyveromyces marxianus, Saccharomyces cerevisiae): they take part in fermentation, produce small amounts of ethanol and carbon dioxide, and may contribute to kefir’s probiotic profile, with effects linked to gut health and immunomodulation.
• Acetic acid bacteria (Acetobacter, Gluconobacter): they take part in fermentation and acetic acid production, associated with gut motility, colonic blood flow, epithelial homeostasis and inflammatory modulation.
• Organic acids, mainly lactic and acetic acid: they acidify the fermented product, support its microbiological stability, and help create an environment less favorable to unwanted microorganisms.
• Bioactive peptides derived from milk proteins: associated with antimicrobial activity, inflammatory modulation, metabolic support, and possible effects on lipid profile and blood pressure.
• Exopolysaccharides (EPS) and kefiran: EPS are sugar polymers produced by microorganisms and released into the surrounding medium. In kefir, they take part in the structure of the grains, the texture of the drink, and biological activities described in experimental models. Kefiran is a specific type of EPS, considered one of kefir’s most characteristic bioactive compounds, with production strongly linked to Lactobacillus kefiranofaciens. It’s associated with antioxidant, antimicrobial, immunomodulatory and anti-inflammatory properties.
• The grains’ biofilm: kefir grains are organized structures formed by microorganisms attached to a matrix that contains EPS, proteins, extracellular DNA and other components. This biofilm organization allows dozens of species to coexist stably and to exchange compounds among themselves, sustaining the diversity and functionality of traditional kefir.
• B-complex vitamins (B1, B12) and minerals: they add to kefir’s nutritional value, building a richer matrix than the original milk.

Comparative studies indicate that artisanal kefir has greater functional potential than industrial kefir, especially in antioxidant activity. This finding is attributed, in part, to the greater microbial and biochemical diversity of artisanal kefir, which can contain phenolic compounds, bioactive peptides, exopolysaccharides and kefiran in more varied concentrations than those found in industrially standardized products.

Mechanistically, these components are associated with:

• Modulation of the gut microbiota and SCFA production
• Support for gut barrier integrity
• Competition with pathogenic microorganisms
• Modulation of inflammatory cytokines
• Antioxidant and antimicrobial activity

During milk kefir fermentation, part of the lactose is naturally transformed. Lactic acid bacteria convert lactose into lactic acid, while enzymes like beta-galactosidase, present in kefir grains, hydrolyze lactose into glucose and galactose. one study showed that the milk’s lactose content dropped from 5.58 g/100 mL to 2.12 g/100 mL after 18 hours of fermentation, and continued falling during refrigerated storage, reaching 0.80 g/100 mL after 7 days at 4 °C. Because of this, fermented kefir tends to have lower lactose content than regular milk, especially when fermentation is extended under refrigeration. Even so, this reduction doesn’t mean all homemade kefir is lactose-free.

Like other fermented foods, kefir delivers, in the same matrix, live microorganisms, fermentation metabolites, bioactive peptides, organic acids, exopolysaccharides and residual lactose, which supports its value as a complete functional food.

Conclusion

Kefir is a traditional fermented food with clinical evidence for modulating the gut microbiota, improving gastrointestinal symptoms, and contributing to lipid profile. It brings together tradition, science and real food in a practical habit. It’s best used as part of a diet based on fresh or minimally processed foods, rich in fiber, fruit, vegetables, legumes and whole grains, with less room for ultra-processed foods.

International and Brazilian guidelines recommend prioritizing whole and minimally processed foods as the basis of the dietary pattern.

• World Health Organization (WHO): Healthy diet - fact sheet
• Harvard T.H. Chan School of Public Health: Healthy Eating Plate
• Brazilian Ministry of Health: Dietary Guidelines for the Brazilian Population