Kefir and the gut microbiome: what it contains and what is supported by evidence
The essentials at a glance
Kefir is created when a community of lactic acid bacteria, acetic acid bacteria, and yeasts ferments a drink. This community lives in kefir grains, a gel-like structure made of sugar chains. Kefir is therefore a fermented food, not a remedy for anything.
This article explains what lives in a kefir grain, how milk kefir differs from water kefir, and where the evidence ends. Whenever a source provides a reference, it is listed here with the authorship and year. Where no reference is available, that is also stated.
First, you will learn how kefir is made and what lives in it. This is followed by symptoms that should be medically evaluated, a comparison of the two types of kefir, a fact check of four common statements, and the question of what an examination of the gut microbiome can contribute.
What to expect in this article
1. What kefir is and how it is made
2. What lives in a kefir grain
3. When abdominal symptoms should be medically evaluated
4. Comparing milk kefir and water kefir
5. What kefir has to do with the gut microbiome
6. Four statements about kefir and what remains of them
7. Where the evidence actually ends
8. Kefir in everyday life: quantity, making it yourself, and tolerability
9. What a microbiome test result shows—and what it does not
10. How you can have your gut microbiome examined
11. Who would benefit from an examination
12. What matters when it comes to kefir
Frequently asked questions
Sources
What kefir is and how it is made
Kefir is a fermented drink. The process behind it is called fermentation and is one of the oldest food-production methods of all: microorganisms break down some of the sugars and produce acids, carbonic acid, and flavor compounds.
What makes kefir special is the starter. With yogurt, a small amount from the previous batch is sufficient; with kefir, you need kefir grains. These are irregularly shaped, gel-like structures that resemble small cauliflower florets.
These grains are added to the liquid, where they work for one to two days, and are then strained out again. They are not used up; they grow instead. The same grains can be reused for years.
Key message
Kefir is not the product of a single type of bacteria, but the result of a community of bacteria and yeasts living together in the kefir grains.
Why kefir tastes different from yogurt
The difference lies in the yeasts. A yogurt culture contains only lactic acid bacteria, whereas kefir also contains yeasts, which produce not only acid but also carbonic acid and small amounts of alcohol.
That is where the slight fizz comes from, which many people notice with their first sip. It is neither an additive nor a fault, but a by-product of fermentation.
The alcohol content remains very low in commercially produced kefir. In homemade kefir, it depends on how long and how warmly it was fermented. Anyone who wants to know the exact amount will find it stated on purchased products, not in their own glass.
Where kefir comes from
Kefir originally comes from the Caucasus, where it was a household drink passed down through generations. The grains were passed on rather than purchased, which is precisely why they still differ from household to household today.
This origin explains a characteristic that is important for evaluation: kefir is not a standardized product. Two glasses from two kitchens do not contain the same microbial community, even if both are called kefir.
What happens during fermentation in the jar
It starts with a liquid containing sugar. In milk kefir, this is milk sugar; in water kefir, it is the added table sugar. Both are food for the cultures.
The microorganisms break down some of this sugar. This produces lactic acid, acetic acid, carbon dioxide, and small amounts of alcohol. The acidity increases, and that is precisely what makes the beverage more shelf-stable than the original liquid.
Fermentation was originally a method of preservation, not a health measure. People fermented foods because there was no refrigeration, and the taste was a side effect they grew accustomed to.
This origin is not a minor detail. It explains why fermented foods occur in almost every food culture, and it serves as a reminder that their widespread presence says nothing about any health effects.
What lives in a kefir grain
A kefir grain is not a living organism but a habitat. It consists of a matrix of sugar chains and proteins in which bacteria and yeasts live side by side.
In milk kefir, this matrix consists primarily of a polysaccharide called kefiran. Tzavaras, Papadelli, and Ntaikou describe it as a heteropolysaccharide made up of roughly equal proportions of glucose and galactose, produced mainly by the bacterial species Lactobacillus kefiranofaciens (Fermentation, 2022).
So the bacterium builds the house in which it lives. This property is why kefir grains grow instead of being consumed, and it distinguishes kefir from any starter culture on the refrigerated shelf.
Bacteria and yeasts working together
Three groups work together in the grain. Lactic acid bacteria break down sugar into lactic acid, thereby increasing the acidity. Acetic acid bacteria produce acetic acid. Yeasts ferment sugar into carbon dioxide and alcohol.
These three groups do not hinder one another; they complement one another. The yeasts provide substances that benefit the bacteria, while the acidic environment created by the bacteria keeps unwanted microbes at bay.
This interplay is exactly what the word “symbiotic” refers to, a term that regularly appears in specialist literature on kefir. It describes a community in which every participant benefits from the others.
Why no two grains are the same
Which species occur and in what quantities depends on the origin of the grain, the temperature, the duration of fermentation, and what it is fed.
This has a consequence for evaluating studies that almost never appears in consumer advice texts. When two studies reach different results, it may be because they simply did not study the same thing.
This point appears again in Chapter 7 because it is the most important limitation of all. Before that, something else belongs here.
What distinguishes the grain from the yogurt cup
An industrial starter culture contains selected strains in known quantities. It is standardized because a manufacturer needs reproducible results.
A kefir grain is the opposite of that. It has grown over decades, adapted to its environment, and contains whatever prevailed there. No one assembled it.
That is both the appeal and the problem. The appeal is that a mature community is more complex than any laboratory mixture. The problem is that it is difficult to make a reliable statement about something unknown.
How many microorganisms it contains
In specialist texts, figures range from a handful to several dozen species per grain. There is no documented figure that applies to kefir in general, because there is no single kefir.
That is why this article does not state a number of species. A rounded figure from a single study would falsely suggest a general validity it does not have.
What can be said is that there are always several groups at the same time, and yeasts are always among them. This distinguishes kefir from all fermented milk products that use only bacteria.
When abdominal symptoms should be evaluated by a doctor
Many people turn to kefir because they have symptoms and are looking for something that might help. That is why this chapter appears near the beginning rather than at the end.
These signs should be evaluated by a doctor
Blood in the stool
reddish, black, or very dark stool, regardless of the amount
Unexplained weight loss
without any change in diet or physical activity
Bowel habits that have changed over several weeks
when the usual pattern changes significantly and permanently
Persistent pain or cramps
in the lower abdomen that do not improve on their own
Fatigue and weakness with pallor
that do not improve with rest
The points follow the compilation by the Institute for Quality and Efficiency in Health Care on intestinal complaints requiring medical evaluation (IQWiG, 2021). The same source notes that all these signs are nonspecific and usually have other causes.
No food is the right answer to any of these points. Anyone who notices them in themselves should make a medical appointment, not look for a remedy in the kitchen cupboard.
Milk kefir and water kefir compared
Both are called kefir and both are made using grains, but they are not the same thing. The differences lie in the substrate, the structure of the grain, and the composition of the microorganisms.
| Criterion | Milk kefir | Water kefir |
|---|---|---|
| Base | Milk, usually cow’s, goat’s, or sheep’s milk | Sugar solution or fruit juice, without milk |
| Grain structure | Kefiran consisting of approximately equal proportions of glucose and galactose | approximately 95 to 97 percent glucose polysaccharides derived from sucrose |
| Microbial balance | Lactic acid bacteria predominate | Yeasts predominate or are present in equal proportions |
| Contains lactose | yes, partially broken down through fermentation | no |
| Taste | tart, creamy, slightly sparkling | light, sparkling, fruity depending on the preparation |
The information about the structure of the grains and the ratio of bacteria to yeasts comes from the review by Tzavaras, Papadelli, and Ntaikou (Fermentation, 2022).
What the difference means in practice
Those who avoid milk are better served by water kefir. Those seeking a creamy consistency should choose milk kefir. This is the simplest rule of thumb, and it has nothing to do with an assumed effect.
A second point concerns sugar. In water kefir, sugar is the food source for the cultures, and some of it remains in the finished beverage. The exact amount depends on the fermentation time and cannot be measured at home.
What kefir has to do with the gut microbiome
Kefir contains live microorganisms. That is why it comes up in connection with the gut microbiome, and it is also where most texts go beyond what has been substantiated.
Documented source
“Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.”
German Nutrition Society (DGE)
Gunda Backes, The Microbiome, Update for Nutrition Counseling, 2026
The sentence defines a term; it does not evaluate a food. It contains two conditions, both of which are significant for kefir: The microorganisms must arrive alive, and they must be present in sufficient quantities.
Whether a particular kefir meets these conditions depends on which cultures it contains, how many there are, and how the beverage was stored. Pasteurized kefir from the shelf is different from freshly prepared kefir made in your own kitchen.
What happens to the cultures in the gut
This is the biggest open question. The sources reviewed for this article do not reveal whether the microorganisms introduced establish themselves permanently in the gut or merely pass through it.
That is why there is no statement about it here. Wording such as “Kefir establishes good bacteria in your gut” would be an unsupported claim, and it does not belong in this text.
What can be said is that kefir provides live cultures, and fermented foods are part of a varied plant- and animal-based diet. The Max Rubner Institute describes the connection between a varied diet and high gut microbiota diversity (MRI, 2026).
Why the amount helps determine the effect
The cited definition contains the phrase “in an adequate amount.” It is easy to overlook, yet it carries half the sentence.
Because it means that a few living cells are not enough. How many would be needed depends on the strain and has not been generally established for kefir.
Anyone who drinks a glass of kefir therefore knows neither which strains they are consuming nor in what quantity. Both are listed on the packaging of a dietary supplement, but not for a cultured food.
The journey through the stomach
Before a culture reaches the colon, it has to pass through the stomach. There, it encounters a highly acidic environment that many microorganisms do not survive.
How many cells from a glass of kefir actually arrive alive is a question for which the sources reviewed provide no information. Advice articles usually skip over it, even though it comes before any question of effects.
That is why this article sticks to description. What is in a glass of kefir can be stated. Where it ends up and what it does there cannot.
Four statements about kefir—and what remains of them
These four statements appear in many texts on the subject. All four sound plausible, and none holds up in the form in which it usually appears.
Checked against the evidence
Commonly claimed
“Kefir builds up the gut flora.”
Supported
In their review, Kusuma and colleagues note that differences in composition, strains, and dosage currently limit the comparability of the available studies. A claim this broad is therefore not supported.
Commonly claimed
“Milk kefir and water kefir are the same thing in two variations.”
Supported
The grains differ fundamentally in their structure, and yeasts predominate in water kefir, unlike in milk kefir (Tzavaras and colleagues, Fermentation, 2022).
Commonly claimed
“The more kefir, the better.”
Supported
The sources reviewed provide no information on a meaningful daily amount. Kusuma and colleagues explicitly point out that standardized dosages still need to be developed.
Commonly claimed
“Kefir helps with joint problems.”
Supported
There are no robust randomized controlled trials of kefir in this area. Only small, open-label pilot studies are available, and nothing more (Kusuma and colleagues).
Behind all four statements lies an understandable wish: that a simple food might solve a persistent problem. The wish is legitimate, but the evidence does not support such a broad claim.
Where the evidence actually ends
There is research on kefir, and there is quite a lot of it. The problem lies not in the number of studies, but in their comparability.
The reason is the same one that makes kefir interesting. Because each grain carries its own community, strictly speaking each study examines a different product. Kusuma and colleagues identify this as precisely the current limit to comparability.
Then there is the question of quantity. Without standardized dosing, a study in which participants drank a specific amount cannot be used to derive a recommendation for everyday life.
A third point concerns sample sizes. Many studies on fermented foods involve a few dozen participants over a few weeks. That is useful for initial indications but insufficient for general recommendations.
Anyone who concludes from this that kefir is ineffective goes just as far as someone who sells it as a solution. Lack of evidence is not evidence to the contrary. It is a gap, and a gap should be identified rather than filled.
What this means for advertising with kefir
In the European Union, health claims on foods may be used only if they have been authorized. As part of this research, no authorized claim for kefir and probiotic cultures could be verified.
That is why this article contains none. Anyone who reads a claim about an effect on a package should check what it is based on, and the same applies to anyone who reads such a claim in a guide.
This is not a statement against kefir. It is a statement about what can and cannot currently be said.
What kefir provides regardless of everything else
Despite all the caution regarding claims about effects, there is one point that does not require a body of studies: milk kefir is a dairy product and therefore provides the nutrients contained in milk.
Kefir contains protein, calcium, and B vitamins because they were present in the milk. This is not an effect of fermentation but a property of the starting product.
Water kefir does not provide this. It is made from sugar water and consequently contains little of it. Anyone who wants to use kefir as a source of nutrients means milk kefir.
Why diversity matters more than a single product
The Max Rubner Institute describes this relationship in terms of the breadth of the diet, not individual foods. A varied diet with different plant-based components is generally associated with greater diversity of the gut microbiota (2026).
For kefir, this means it can be one component of this diversity, just like sauerkraut, yogurt, or pickled vegetables. As a single component, it contributes no more and no less than the others.
Anyone who drinks kefir every day but otherwise eats an unbalanced diet has one fermented component and an unbalanced diet. The calculation does not add up, and that is not an opinion but the logic of the cited statement.
Kefir in everyday life: quantity, making it yourself, tolerability
When the available studies do not provide a dosage, the practical answer is: Kefir is a food, and foods should be consumed according to tolerance and taste.
Kefir is a food, and foods should be consumed according to tolerance and taste.
Anyone starting out should begin with a small amount. A fermented beverage with live cultures and carbonation can initially cause bloating, which says nothing about an intolerance.
Making kefir yourself
To make it yourself, you need kefir grains, a clean glass jar, the right liquid, and time. Put the grains in, leave the jar at room temperature, and strain it after one or two days.
Two things are important here. Cleanliness, because open fermentation also gives unwanted germs an opportunity. And patience, because the first batches usually taste different from later ones as the culture adapts to its new environment.
If you are unsure whether a batch is still good, judge it by its smell and appearance. Kefir that smells rotten or shows mold should be discarded. The same rule applies to any other food.
The fermentation time controls the taste. Shorter means milder and sweeter because less sugar has been broken down. Longer means more sour and fizzy because more acid and carbon dioxide have formed.
Temperature also plays a role. In a warm summer room, the same amount ferments noticeably faster than in a cool winter room. Anyone who follows the clock instead of the taste will get very different results over the course of the year.
Buy or make your own
Both options have their merits, and the decision depends less on the result than on the effort involved. Store-bought kefir is immediately available, consistent in taste, and transparent in its labeling.
Homemade kefir costs almost nothing after the initial purchase and allows you to control its acidity. In return, it requires regular attention: A culture left without care for two weeks does not always survive.
One distinction matters when it comes to live cultures. If store-bought kefir was heated after fermentation, the cultures are no longer alive. Whether this is the case is stated on the packaging, usually in the fine print.
Who should exercise caution
For people with severely weakened immune systems, handling live cultures is a question for a medical professional, not a guidebook. The same applies during pregnancy to homemade beverages.
People who have trouble tolerating lactose may get better results with water kefir. Milk kefir still contains lactose, even though some of it is broken down during fermentation. How much remains depends on the batch.
What a microbiome test shows and what it does not
A natural question is: Can I measure whether kefir is changing anything for me? The honest answer has two parts.
A microbiome report shows which bacteria are present and in what proportions. Anyone who measures before making a change and again three months later can see whether the composition has shifted.
What such a comparison does not show is the cause. If during these three months you drank kefir, ate more vegetables at the same time, and experienced less stress, the report does not say which of these factors had an effect.
What a sound observation would look like
Anyone who really wants to know whether kefir changes anything for them needs three things: a baseline, as much of the rest of their diet kept constant as possible, and a second measurement after several months.
The second point is the most difficult. In everyday life, many things change at the same time, and each of these changes affects the gut flora. That is why everyday observation rarely provides a clear answer.
A more realistic question is: How do you feel about kefir? Do you tolerate it, do you like the taste, does it fit into your day? You can answer these questions without a laboratory, and for a food, they are the right ones.
How this article differs from its neighbors
This text explores one food in depth and explains its composition. Anyone looking for a more general overview will find it in Understanding Kefir for Health. Anyone interested in the dairy-free version will find it in Understanding Water Kefir.
You can look up in advance which bacterial species and markers may appear in a report. The Gut Encyclopedia lists them in a searchable overview.
Chapter at a glance
A microbiome report can show whether the composition of the gut flora has shifted between two measurements. It cannot show which of several simultaneous changes caused this shift. Anyone who wants to observe kefir specifically should change as little else as possible during this period.
How you can have your gut flora analyzed
Anyone who wants to see the composition of their own gut flora can have it determined using a stool sample. The mybody®x Gut Microbiome Test (MYBODY Lab GmbH) reads the genetic material of the microorganisms in the sample.
What it does not reveal is stated on the card itself.
Gut test from a stool sample
Gut microbiome test | Complete
Detects more than 1,500 bacterial species through DNA sequencing, along with biodiversity, enterotype, FODMAP index, and eight bioindicators. What the test does not do: It does not measure whether cultures from a food have reached the gut, and it does not establish kefir consumption. It does not provide a diagnosis or detect inflammatory bowel disease, tumors, infections, or celiac disease.
Laboratory analysis: 5–10 business days after receipt of the sample
Information from the product page, accessed on 27 August 2026
The figure of more than 1,500 bacterial species comes from the product page. The specific species and markers are listed in the Gut Lexicon.
Who should consider having a test
Useful for you if …
you are planning a dietary change and want to track its progress with a measurement before and another after three months.
your symptoms have persisted for months and have been medically evaluated.
you want to see what your gut microbiome currently looks like after antibiotic therapy.
Probably not if …
you want to know whether kefir works for you. No test result can answer that because it cannot attribute the cause of a change.
you notice one of the warning signs from Chapter 3. Then the appointment comes first.
you do not want to change anything about your diet in the coming months. Then there is no point of comparison.
What matters when it comes to kefir
If you take away just one action from this article, let it be this: Try kefir in a small amount for two weeks and pay attention to how well you tolerate it. The current evidence does not provide any stronger basis for a decision.
This is unspectacular, but it is honest. Kefir is an old, well-preserved, nutrient-rich food with live cultures. What else it does in the body has not been established to the extent claimed by many texts.
What does hold up is the context. Kefir is one component of a varied diet, not a replacement for one. Anyone who sees it as a supplement will not be disappointed. Anyone who sees it as a solution will be.
And anyone who puts off seeing a doctor because a food might fix the problem as well is losing time. This is the only point in this article that is about more than taste.
At first, the question was what kefir has to do with the gut microbiome. The most honest answer is: It brings its own microbial community with it. What this community does in your gut, nobody currently knows exactly—and anyone who writes otherwise doesn’t know either.
Frequently asked questions
What exactly is kefir?
Kefir is a fermented drink made with kefir grains. These grains consist of a matrix of sugar chains and proteins in which lactic acid bacteria, acetic acid bacteria, and yeasts live together. In milk kefir, the matrix consists mainly of kefiran, a polysaccharide made up of glucose and galactose (Tzavaras and colleagues, Fermentation, 2022). The grains are strained after fermentation and reused.
What is the difference between milk kefir and water kefir?
Milk kefir is made with milk, while water kefir is made with a sugar solution or fruit juice. The grains differ fundamentally: Water kefir grains consist of approximately 95 to 97 percent glucose polysaccharides derived from sucrose, while milk kefir grains consist of kefiran. Yeasts predominate in water kefir or are present in equal proportions, while lactic acid bacteria predominate in milk kefir (Tzavaras and colleagues, 2022).
How much kefir should you drink per day?
There is no substantiated information on a sensible daily amount. The scientific literature explicitly points out that standardized dosages still need to be developed. In practical terms, this means that kefir is a food and should be consumed according to personal tolerance and taste. Those starting with it should begin with a small amount, as a fermented drink can initially cause bloating.
Do the bacteria from kefir colonize the gut?
This cannot be determined from the sources reviewed for this article. This does not answer whether microorganisms that are introduced remain permanently in the gut or merely pass through it. For this reason, statements such as “kefir colonizes good bacteria” do not appear in this text. It is established that kefir contains live cultures and that a varied diet is associated with high gut microbiota diversity (MRI, 2026).
Can I use a test to measure whether kefir works for me?
Only to a limited extent. A microbiome report shows how the gut flora is composed at a given point in time. Two measurements taken three months apart show whether anything has shifted. However, they do not show which of several simultaneous changes was responsible. Anyone who wants to monitor kefir specifically should change as little else as possible during this period.
Next step
Look it up first, then decide
Before deciding on an examination, you can check the Gut Encyclopedia to see which markers a report contains. Anyone who wants to monitor a dietary change can use the Gut Microbiome Test as a starting point.
Go to the Gut Encyclopedia Go to the Gut Microbiome TestRead more
You might also be interested in this
What these two groups of bacteria do in the gut and where they come from.
The dairy-free version, with your own starter culture and your own taste.
The searchable overview of all markers that may appear in a test report.
Sources
- German Nutrition Society (DGE), Gunda Backes: The Microbiome, Update for Nutritional Counseling (2026) – dge.de
- Tzavaras D., Papadelli M., Ntaikou I.: From Milk Kefir to Water Kefir, Assessment of Fermentation Processes, Microbial Changes and Evaluation of the Produced Beverages. Fermentation 8(3):135, 2022 – mdpi.com
- Max Rubner Institute (MRI), German Federal Research Institute of Nutrition and Food: Scientific classification of dietary fiber (as of June 2026) – mri.bund.de
- Institute for Quality and Efficiency in Health Care (IQWiG): Signs of colorectal cancer (as of 2021) – gesundheitsinformation.de
The verbatim quotation defining probiotics comes from source [1] and provides a definition of the term, not an assessment of kefir. The information on the structure of kefir grains, the proportion of glucose polysaccharides in water kefir grains, and the ratio of yeasts to lactic acid bacteria comes from [2]. The statement on the diversity of plant foods and the diversity of the gut microbiota comes from [3]. The warning signs in Chapter 3 follow [4]. The limitations regarding the comparability of kefir studies, the lack of standardized dosages, and the lack of randomized studies in the area of joint health mentioned in the fact check and Chapter 7 come from the review by Kusuma and colleagues in Frontiers in Food Science and Technology; the publication dates are inconsistent on the publisher’s website, so no year is given here. Information on price, marker range, sample type, and laboratory comes from the mybody®x product page, accessed on 27.08.2026; processing times follow the central specification for gut tests. All sources were accessed and reviewed on 27.08.2026.
mybody®x Editorial & Specialist Team
Microbiome science Nutritional science Gut science Laboratory diagnostics
This article was created by the mybody®x editorial and specialist team. The team combines microbiome and gut science, nutritional science, and laboratory diagnostics. Anyone who contributes to it is listed on the authors’ page.
Published on 27.08.2026 · Last updated on 27.08.2026
The content is intended for general information and does not replace medical advice, diagnosis, or treatment. Reference ranges depend on the laboratory, method, and age—your test report always takes precedence.
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