Dog gut microbiome: what it is and why it matters

Billions of bacteria live in your dog’s gut. You cannot see them, but they work for your dog every single day. Scientists call this community the gut microbiome, and sometimes describe it as an “invisible organ”.

What is the gut microbiome

The gut microbiome is a varied community of microbes, mainly bacteria, living in a dog’s digestive tract. It is not a random mixture. The bacteria cooperate, compete for food and produce substances the dog’s body uses. It looks a little different in every dog and changes with diet, medication and age.

What is the dog microbiome made of?

Most bacteria in a dog’s gut belong to five phyla: Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria (review by Pilla and Suchodolski, 2020). In a study of 29 pet dogs, the three largest phyla, Bacteroidetes, Firmicutes and Fusobacteria, each made up more than 20% of the bacteria on average (Kubinyi et al., 2020).

The exact make-up differs from dog to dog. Two groups play a special role:

• Faecalibacterium. It is one of the bacteria that produce short-chain fatty acids (Pilla and Suchodolski, 2020). In a study of 13 healthy dogs and 13 dogs with acute diarrhoea, the dogs with diarrhoea had fewer of these bacteria (Guard et al., 2015).
• Peptacetobacter hiranonis (formerly Clostridium hiranonis). According to a review, it is key for converting bile acids (Németh et al., 2026). It is also one of the seven bacterial groups, along with the total amount of bacteria, used to calculate the Dysbiosis Index (AlShawaqfeh et al., 2017).

Where it lives and what it does

• Large intestineThis is where most bacteria live. It is their main “workplace”.Pilla and Suchodolski, 2020
• Butyric acidBacteria make it from fibre. It is the main fuel for the cells of the large intestine.Pilla and Suchodolski, 2020

The microbiome helps your dog process food it could not digest on its own, and it is part of the body’s defences. The immune system “learns” from the gut bacteria what is fine and what is not.

What does the dog microbiome do?

The main roles of the dog gut microbiome

Area	What the microbiome does
Fibre digestion	Bacteria break down fibre that the dog cannot digest itself and make short-chain fatty acids from it, such as butyric acid (Pilla and Suchodolski, 2020).
Bile acids	Bacteria convert bile acids from the liver into their secondary forms. After metronidazole, there were fewer of them in the stool of healthy dogs (Pilla et al., 2020).
Immunity	Gut bacteria “teach” the immune system to tell what is harmless (Pilla and Suchodolski, 2020).
Gut protection	According to a review, the microbiome helps protect against pathogens, meaning bacteria that can cause problems (Pilla and Suchodolski, 2020).

How does the dog microbiome differ from ours?

The dog microbiome is more similar to the human one than the microbiomes of pigs or mice are. This comes from the work of Coelho et al. (2018), which compared the gut metagenomes of dogs, humans, mice and pigs and built a catalogue of 1,247,405 genes of the dog microbiome.

The response to food was similar too. In the same study, two different diets had a large and repeatable effect on the microbiome of dogs, regardless of breed or sex, and the responses matched earlier studies in humans. In overweight dogs, the shifts after a high-protein diet were larger than in lean dogs.

Still, a dog is not a small human, and what works for people may not work for dogs. So do not transfer human data to your dog without checking it.

Gut, skin and behaviour

Research on the dog microbiome is developing quickly, and the first studies suggest the gut is linked to other parts of the body too:

• Skin. In a small pilot study, dogs with atopic dermatitis (12 dogs) had a different gut bacteria make-up from healthy dogs (20 dogs), which suggests a link between the gut and the skin (Sugita et al., 2023). In some dogs, skin problems may also be connected with the gut. But the cause of itching is always for a vet to determine.
• Behaviour. In two smaller studies (31 and 42 dogs), dogs with aggression or fears had a different gut bacteria make-up from dogs without these problems (Kirchoff et al., 2019; Mondo et al., 2020). This is an association, not proof that the bacteria cause the behaviour. Research here is only just beginning.

What is dysbiosis and the Dysbiosis Index?

Dysbiosis is an imbalance of gut bacteria in which the composition of the microbiome changes, and with it the substances the bacteria produce (Pilla and Suchodolski, 2020). It is not a disease in itself. The article Dysbiosis in dogs: causes, signs and what to do covers it in detail.

The Dysbiosis Index is a laboratory calculation that expresses the degree of dysbiosis as a single number from one stool sample. It is based on the total amount of bacteria and seven bacterial groups, including Faecalibacterium, Fusobacterium and Peptacetobacter hiranonis. In the work of AlShawaqfeh et al. (2017), with 95 healthy dogs and 106 dogs with chronic inflammatory bowel disease, the index told the two groups apart with 74% sensitivity and 95% specificity. A negative value means a normal state, a positive one dysbiosis.

The test does not tell you why the microbiome is changed, and it does not replace an examination. You will find what to expect from a test, and what not to, in the article Dog microbiome test: what a stool analysis can show.

How can you tell that a dog’s microbiome is out of balance?

You cannot tell reliably at home. You cannot see the microbiome, only what happens around it. In studies, dysbiosis was found in dogs with acute diarrhoea (Guard et al., 2015), in chronic gut diseases and after antibiotics (Pilla and Suchodolski, 2020). That is why these digestive signs are linked with it:

• Soft stool or diarrhoea that keeps coming back or will not go away. How to read stool is explained in the article Dog poop: what colour, shape and consistency reveal.
• Alternating firm and loose stool, mucus or a changed smell of the poop.
• Gas and rumbling in the belly, especially when they appear after antibiotics or after a change of food.
• Vomiting, a weaker appetite or weight loss, which need a vet straight away.

Note: none of this is proof of dysbiosis. The same signs can be caused by parasites, food intolerance or inflammation of the pancreas, and nobody can tell them apart from dysbiosis at home. The cause is for a vet to determine. What to do about diarrhoea is summed up in the article Diarrhoea in dogs: what to do and when to see a vet, and you will find a wider overview in the article Digestive problems in dogs: signs, causes, what to do.

Balanced microbiome vs. dysbiosis: what changes in studies

Marker	Balanced	In dysbiosis
Diversity	A varied community of bacteria.	Lower richness and diversity of bacteria in dogs with acute diarrhoea (Guard et al., 2015) and with chronic gut disease (Pilla and Suchodolski, 2020).
Peptacetobacter hiranonis (formerly Clostridium hiranonis)	The main bacterium that converts primary bile acids into secondary ones in a dog’s gut.	Decreases. About 50 to 60% of dogs with chronic gut disease have this bacterium reduced (Suchodolski, 2021).
Secondary bile acids	Formed by converting the primary ones, they help keep some unwanted bacteria in check.	There are fewer when P. hiranonis decreases (Suchodolski, 2021). After 14 days of metronidazole, there were fewer of them in the stool of healthy dogs (Pilla et al., 2020).
Faecalibacterium and Fusobacterium	Commonly present.	Typically decrease (Suchodolski, 2021). Dogs with acute diarrhoea had less Faecalibacterium (Guard et al., 2015).
E. coli and Streptococcus	A small share, a normal part of the gut.	The share typically rises (Suchodolski, 2021). What matters is the balance, not mere presence.
Dysbiosis Index	A negative number.	A value above 2 is now considered dysbiosis, and values from 0 to 2 are borderline and mean a mild shift (Suchodolski, 2021).

The table is not a diagnostic guide either. The Dysbiosis Index does not make a diagnosis: in one larger study, about 36% of 146 dogs with chronic gut disease had a normal value (Sung et al., 2023). The number shows the state of the bacteria, not the cause.

How do diet and age change the dog microbiome?

Diet changes the composition of the dog microbiome quickly and markedly. In 11 healthy adult dogs, a gradual switch from dry food to a diet high in cooked ground beef caused changes in the bacteria in the stool. After the dogs went back to kibble, the make-up largely returned to normal (Herstad et al., 2017). That is why stability and gradual changes matter, as we explain in the article Switching dog food: a 7 to 10 day plan. Fibre, the main “food” for gut bacteria, is covered in Fibre for dogs: what it does and when to add it.

Age plays a role too:

• Puppies. Around weaning, with the move from milk to solid food, a puppy’s microbiome gradually becomes more similar to that of adult dogs. The changes continue until adulthood, though (review by Balouei et al., 2023).
• Seniors. In a study of 29 pet dogs, older dogs had a lower proportion of Fusobacteria (Kubinyi et al., 2020), but it was a small cross-sectional study. Another study, based on culturing bacteria from stool, reported that lactobacilli tend to decline in older dogs (Masuoka et al., 2017).

What throws the microbiome off balance

1. Antibiotics. They also hit the “friendly” bacteria, and the gut may then take several weeks to recover. After 14 days of metronidazole in healthy dogs, some changes, such as a drop in Fusobacteria, had not fully disappeared even four weeks after stopping it (Pilla et al., 2020). Antibiotics are often essential, so give them exactly as your vet directs. You will find more in the article Dog after antibiotics: how to support your dog’s tummy.
2. A sudden change of food. When you swap your dog’s food overnight, the bacteria have to adapt fast. A study in healthy dogs showed that diet changes the bacteria in the stool, even when the change is gradual (Herstad et al., 2017). Switch to a new food gradually, over several days.
3. Gut diseases. In chronic gut diseases, the make-up of the bacteria is often altered. This is a case for a vet.

What can you do for your dog’s microbiome?

The main things you can do at home for your dog’s microbiome are to keep to a stable, good-quality food, change it gradually, avoid tackling problems on your own and keep an eye on the stool.

• Stable food. If it suits your dog, do not change it needlessly often.
• Gradual changes. Mix the new food in bit by bit, not overnight. You will find a guide in the article Switching dog food: a 7 to 10 day plan.
• Antibiotics only as your vet directs. Do not give them “just in case” and never stop them without talking to your vet.
• Supplements only after advice. Whether a probiotic makes sense is for your vet to decide. You will find an overview in the article Probiotics for dogs: what they are and how to choose.
• Keep an eye on the poop. It is the cheapest indicator of what is going on in the gut. How to read it is explained in Dog poop: what colour, shape and consistency reveal.

If digestive problems or itching keep coming back, book your dog in for an examination even if nothing is acute. The microbiome is only one piece of the puzzle, and there can be several causes. The article Soft stool in dogs: causes and what to do is about stool that stays soft.

How the microbiome can be assessed

The make-up of the microbiome can be determined from a stool sample. An analysis shows which bacteria live in the gut and how their make-up differs from the usual. You will find what to expect from such a test, and what not to, in the article Dog microbiome test: what a stool analysis can show.

Frequently asked questions

What is the dog microbiome?

The dog microbiome is the community of bacteria and other microbes living in a dog’s digestive tract, mostly in the large intestine. It helps with digesting fibre, converts bile acids into their secondary forms and is part of the body’s defences. It looks a little different in every dog and changes with diet, medication and age.

Where in a dog’s body do most bacteria live?

In the large intestine. The number and variety of bacteria in the digestive tract increase from the stomach onwards, and in the large intestine bacteria that do not need oxygen predominate. From fibre they make short-chain fatty acids, for example butyric acid, which the cells of the large intestine use as their main source of energy.

What throws the dog microbiome off balance?

Most often antibiotics, a sudden change of food and gut diseases. In a study of healthy dogs, some changes after metronidazole were still visible four weeks after stopping it. Antibiotics are often essential, though, so always give them exactly as your vet directs. Change food gradually and have repeated problems checked.

Which bacteria live in a dog’s gut?

Most belong to five phyla: Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. In a study of 29 pet dogs, Bacteroidetes, Firmicutes and Fusobacteria each made up more than a fifth of the bacteria on average. The exact make-up differs from dog to dog and changes with diet, age and medication.

Is the dog microbiome similar to the human one?

In gene content, it is closer to it than the microbiomes of pigs or mice. According to a 2018 study, the dog microbiome responded to a change of diet in a similar way to what earlier studies described in humans. Still, it is a different species, and what holds for people may not hold for your dog. Do not transfer human data to your dog without checking it.

What is dysbiosis in a dog?

Dysbiosis is an imbalance of gut bacteria in which both the make-up of the microbiome and the substances the bacteria produce change. It is not a disease in itself, but a state that accompanies many digestive problems. A lab can express it as the Dysbiosis Index, where a negative value means a normal state. But the cause is always for a vet to determine.

Can a dog’s microbiome be restored?

Nobody can promise it. Once the disturbing factor is removed, the composition often moves back towards the original, but not always, and differently in each dog. After a switch back to dry food, the changes caused by the diet change largely reversed (Herstad et al., 2017), and after metronidazole some changes had not disappeared even after four weeks (Pilla et al., 2020). What helps is a stable diet and your vet.

Sources

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