Beneficial bacteria and probiotics for dogs: how to support the microbiome?

In recent years, probiotics have become an almost universal recommendation. Dog has diarrhea? Probiotic. Antibiotic course? Probiotic. Gas? Probiotic. Sensitive digestion? Probiotic. Immune support? Probiotic again.

But a dog’s gut is not an empty apartment that simply needs as many “good bacteria” moved in as possible.

It already contains an enormous microbial community: bacteria, fungi, viruses and other microorganisms. They interact with one another, use compounds from food and produce metabolites that, in turn, interact with the intestinal wall, immune system and other organ systems.

This community of microorganisms is called the microbiota. The broader term microbiome includes the microorganisms, their genetic material and the surrounding microbial environment.

That is why there is one idea in the integrative approach that I especially like: before asking which bacteria we should add, it is worth asking what kind of environment the dog’s existing microbes are living in.

There is little point in sowing seeds if the soil does not support them.

What is a probiotic?

A probiotic is a live microorganism that, when administered in adequate amounts, confers a health benefit on the host.

There are three important parts to that definition:

• the microorganism must be alive;
• there must be enough of it;
• a health benefit must be demonstrated.

This means that not every bacterium in a jar, yogurt or fermented food is automatically a probiotic in the scientific sense. Something also does not become a probiotic simply because the manufacturer prints the word on the label.

Even more importantly, probiotic effects can be strain-specific.

If one particular strain of Lactobacillus, Bifidobacterium or Enterococcus has shown a beneficial effect in a study, we cannot automatically assume that every other strain of the same species will do exactly the same thing in a dog.

This is one of those places where marketing tends to run faster than science. A label may list ten bacterial species and one hundred billion CFU, which looks impressive. But ten strains are not automatically better than one, and one hundred billion are not automatically better than one billion.

The more useful question is: has this particular strain, at this particular dose, been studied for the purpose we want to use it for?

What do we actually know about probiotics in dogs?

In dogs, probiotics have been studied in acute diarrhea, gastroenteritis and several other gastrointestinal problems.

Some studies have found a benefit, in others the effect has been small, and in some there has been no meaningful difference from the control group.

That does not necessarily mean the studies contradict one another. They simply use different microorganisms, strains, doses, preparations and very different dogs.

For example, one double-blind placebo-controlled study in dogs with acute diarrhea used a combination of three canine-derived Lactobacillus strains. Stool consistency normalized in the probiotic group and appetite was better maintained. But that result applies to the combination that was actually studied, not automatically to every probiotic on the market.

Veterinary reviews published in 2024 likewise note that the use of “biotics” is promising, but many questions remain about choosing the right product, optimal amounts, mechanisms and use in different diseases.

So, based on what we know today, it is more accurate to say: some probiotic strains may be useful for dogs in certain situations.

Not: every probiotic helps every dog.

Does a probiotic have to live permanently in the dog’s gut?

No.

This matters because older discussions of probiotics sometimes created the impression that a successful probiotic is only a bacterium that arrives in the gut, unpacks its suitcase and settles there for good.

In reality, many probiotic microorganisms may only be temporary visitors in the gastrointestinal tract.

That does not make them useless. While passing through the gut they may influence other microorganisms, metabolism, the intestinal environment and the host’s responses.

So we cannot call a probiotic “money flushed down the toilet” simply because the microorganism does not permanently colonize the dog’s gut. This is exactly where the strain matters, and so does the job we expect it to do.

So what is a “beneficial bacterium”?

In everyday language it is perfectly understandable to talk about good and bad bacteria. Biologically, the picture is much more complicated.

A microorganism is not necessarily always “good” or always “bad” in every situation. Its function, abundance, location, relationships with other microorganisms and the dog’s own health all matter.

A healthy microbiome therefore does not simply mean having as many so-called good bacteria as possible.

What matters is how the whole ecosystem functions.

A prebiotic is not a bacterium

This is where the terminology often gets mixed up.

A probiotic is a live microorganism.

A prebiotic is a substrate that is selectively utilized by host microorganisms and whose use confers a health benefit.

Put simply, a prebiotic can be thought of as food for the microbes we want to support.

But we still need to be precise.

Not every type of fiber is automatically a prebiotic. The scientific definition requires both selective utilization by microorganisms and a health benefit.

Depending on the context, prebiotic or readily fermentable substrates may include, for example:

• inulin;
• fructooligosaccharides;
• galactooligosaccharides;
• certain resistant starches;
• other fermentable compounds with specific properties.

This is where food becomes especially interesting from an integrative point of view.

Instead of only adding new microorganisms, we can also influence what the microbes already living there have available to eat.

Should prebiotics and probiotics come from a supplement or from food?

For me, “real food or a preparation” is not a particularly useful either-or question. They are not opposites.

If a dog has a specific clinical problem and there is a well-studied probiotic strain at a defined dose for that problem, a standardized preparation has a very clear advantage: we know much more precisely what we are giving.

If the goal is long-term support of the microbiome in a healthy dog, a food-based approach can be at least as interesting.

In integrative veterinary medicine, the gut environment may be supported with, for example:

• different suitable fibers;
• vegetables and plant ingredients;
• resistant starch;
• fermented foods;
• kefir;
• fermented goat’s milk.

The point is not that these foods “treat the microbiome”. The point is that food shapes the environment in which the dog’s microorganisms live every single day.

Kefir and fermented foods

Kefir is one of my favorite examples of why food and a standardized probiotic are not quite the same thing.

Kefir can contain different bacteria and yeasts at the same time, as well as compounds they produce and nutrients altered by fermentation.

That is a much more complex biological system than a capsule containing one or two selected bacterial strains.

Kefir has also been studied in dogs.

In a very small 2019 study, six healthy adult dogs were given kefir for two weeks and changes were observed in the fecal microbiome. The study was far too small, however, to support broad clinical conclusions.

In 2023, researchers compared traditional kefir, commercial kefir and a control in 12 healthy dogs. The microbial composition of the kefir products differed considerably, while the overall effects on the dogs’ fecal microbiome and metabolites were relatively modest.

A useful reminder: more microbes do not automatically mean more health benefit.

At the same time, a modest change in the microbiome does not mean fermented food has no value.

Food can have many effects beyond how dramatically it changes the bacterial profile in a single stool sample.

Is every fermented food a probiotic?

No.

A fermented food may contain live microorganisms, but to call it a probiotic in the scientific sense, a health benefit must have been demonstrated for specific microorganisms used in adequate amounts.

So kefir can be a very interesting fermented food without every glass of homemade kefir qualifying as a standardized probiotic.

Resistant starch: a good example of why “more” is not always better

Resistant starch is not fully digested in the small intestine and reaches the large intestine, where microorganisms can use it.

One food-based source is green, or unripe, banana.

Resistant starch from banana flour has also been studied in dogs. It changed the composition of the microbiome, but not every change automatically moved in a direction we could simply label “better”.

It is a good example of why “fermentable”, “high-fiber” or “prebiotic” does not automatically mean that more is better.

The Homeostasis Fairy reminds us: amount, form, the rest of the diet and the individual dog’s tolerance all matter.

What about garlic?

Garlic contains fructans, among other compounds, so its possible effects on gut microbes are biologically interesting.

However, direct clinical evidence for using garlic as a prebiotic in dogs is limited, and when it comes to safety, dose, form and the individual animal matter.

In FendaF’s article “Garlic and dogs” we take a separate look at dose, toxicology and practical use.

For this discussion, the main point is that there is a difference between a small food ingredient, a therapeutic amount and a very large experimental dose. None of those differences justify a simplistic slogan such as “garlic is always good” or “garlic is poison at any dose”.

What is a synbiotic?

In everyday language, people often say: probiotic + prebiotic = synbiotic.

That is a useful memory aid, but the scientific definition is a little more precise.

A synbiotic is a mixture of live microorganisms and a substrate selectively utilized by microorganisms that together confer a health benefit on the host.

ISAPP also distinguishes complementary and synergistic synbiotics. So simply mixing bacteria and fiber does not automatically create a well-supported synbiotic.

And what is a postbiotic?

Postbiotics are one of the newer concepts and have already become very popular in marketing.

According to the ISAPP definition, a postbiotic is a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host.

Important: a dead bacterium is not automatically a postbiotic.

A purified microbial metabolite alone is not automatically a postbiotic under this definition either.

One practical advantage of postbiotics is that a live microorganism does not have to survive production, transport and storage.

But in veterinary medicine there is no reason to declare them the next miracle solution just yet.

A 2025 systematic review of postbiotics in dogs identified 13 in vivo studies. In pooled analyses of selected outcomes, no statistically significant difference was found between postbiotic and control groups, and the evidence was limited by small samples, different preparations and differing study designs.

In other words: an interesting and developing field, not miracle powder.

Probiotics and antibiotics

The effect of an antibiotic on the microbiome begins during treatment, not only after the last tablet has been given.

Antibiotics are used for a reason and should not be avoided when they are genuinely needed.

At the same time, antibiotics can affect not only their target organisms but also the composition and function of the gastrointestinal microbial community. That is why microbiome recovery and appropriate antibiotic use are increasingly discussed together.

Whether a particular dog benefits from a probiotic, prebiotic food, synbiotic or another strategy during or after treatment depends on the situation.

It also does not make sense to automatically give every live bacterium at exactly the same time as an antibiotic. Timing depends on both the antibiotic and the microorganism, so the instructions for the specific product matter.

Supporting the microbiome is not only about supplements

This brings us back to the integrative view.

A dog’s digestive tract does not live separately from the rest of the body. The microbiome can be influenced by:

• food and dietary variety;
• different fibers;
• medications;
• infections and diseases;
• age;
• environment;
• physical activity;
• stress;
• other individual factors.

That is why, to me, it is strange to talk about supporting “gut health” with one capsule while ignoring the whole rest of the picture.

If a dog is under chronic stress, has ongoing gastrointestinal symptoms or is eating a diet that does not suit them, one probiotic should not be expected to fix the whole system.

When might a probiotic be worth considering?

Not simply because probiotics are “healthy”.

The first question I would ask is: what are we actually trying to achieve?

Is the goal:

• support during acute diarrhea;
• microbiome support during or after antibiotic treatment;
• adding support to the treatment plan of a dog with a chronic gastrointestinal problem;
• a stressful period;
• a diet change;
• or long-term microbiome support in an otherwise healthy dog?

These are not the same situation. With chronic symptoms, a probiotic should not become a nice-looking jar that allows the underlying cause to remain unexplored.

If the dog:

• vomits repeatedly;
• has chronic or recurrent diarrhea;
• is losing weight;
• has blood in the stool;
• has severe pain or another persistent gastrointestinal symptom,

the cause needs to be investigated.

Microbiome support can be part of a treatment plan, but it does not replace a diagnosis.

Does a healthy dog need a probiotic every day?

Not necessarily. And this may be the most important point in the entire article.

A healthy dog eating a varied diet that suits them does not automatically need a scoop of probiotic powder every morning for the rest of their life.

For one dog, a specific well-studied probiotic may be an excellent solution. For another, kefir or another well-tolerated fermented food may be more useful. For a third, it may be worth looking at whether the diet contains enough suitable fiber.

Sometimes these approaches are used together. And sometimes nothing extra is needed at all.

Gut health does not fit into a single capsule

A probiotic can be an excellent tool. But the question should not only be which bacteria we are adding to the dog.

Just as important, and sometimes more important, is the question: what kind of environment are we creating every day for the dog’s own microbiome?

Probiotics provide specific live microorganisms.

Prebiotics support microorganisms with suitable substrates.

Synbiotics combine these approaches.

Postbiotics show that a microorganism does not necessarily even have to be alive for a health benefit to be possible.

Fermented foods add a whole food matrix to the picture, together with microorganisms and their metabolic products.

So for me the question is not: “a supplement or real food?”

A better question is: what are we trying to achieve, how much evidence do we have for this particular approach, and does it suit this particular dog?

And perhaps most importantly: the microbiome does not only need to be bought. It also needs to be fed.

Sources

• ISAPP. Probiotics, Prebiotics, Synbiotics, Postbiotics and Fermented Foods Defined. Link
• Gómez-Gallego C et al. A canine-specific probiotic product in treating acute or intermittent diarrhea in dogs: A double-blind placebo-controlled efficacy study. Veterinary Microbiology. 2016;197:122–128. PMID 27938673. Link
• Wilson SM, Swanson KS. The influence of ‘biotics’ on the gut microbiome of dogs and cats. Veterinary Record. 2024. PMID 39545542. Link
• Salavati Schmitz S. Evidence-based use of biotics in the management of gastrointestinal disorders in dogs and cats. Veterinary Record. 2024. PMID 39545596. Link
• Schmid SM, Tolbert MK. Harnessing the microbiome: probiotics, antibiotics and their role in canine and feline gastrointestinal disease. Veterinary Record. 2024. PMID 39545593. Link
• Kim DH et al. Modulation of the intestinal microbiota of dogs by kefir as a functional dairy product. Journal of Dairy Science. 2019;102:3903–3911. PMID 30827566. Link
• Metras BN et al. Effects of commercial and traditional kefir supplementation on healthy adult dogs. Journal of Animal Science. 2023;101:skad316. PMID 37742216. Link
• Schmitz SS et al. Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial. Access Microbiology. 2024;6:000774.v4. PMID 38868374. Link
• Salminen S et al. The ISAPP consensus statement on the definition and scope of postbiotics. Nature Reviews Gastroenterology & Hepatology. 2021;18:649–667. PMID 33948025. Link
• Bonel-Ayuso DP et al. Effects of Postbiotic Administration on Canine Health: A Systematic Review and Meta-Analysis. Microorganisms. 2025;13:1572. PMID 40732081. Link

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