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Why every dog has a different microbiome and what shapes it
Every dog’s microbiome differs, shaped by age, diet, origin and drugs. In a study of 35 dogs, the dog itself explained 39% of differences. Studies 2018 to 2026.
You have two dogs at home, the same food, the same walk. One is completely fine after a new treat, the other has mushy poop the next day. One possible explanation lies in the gut: the bacteria that live there differ from dog to dog. In 2026 two large studies came out that show how much, and how much science still does not know.
- A dog’s gut microbiome is the community of bacteria in the dog’s gut, and its make-up is a little different in every dog.
- In a study of 35 healthy dogs, the individual dog accounted for 39% of the differences between stool samples (Rojas et al., 2026).
- Its composition is shaped by age, diet, origin, environment and medication, but the evidence is of different strength for each of these factors.
- In a study of 922 dogs, bacterial diversity fell with age and dogs became less and less similar to each other (Bamberger et al., 2026).
- A microbiome test describes the composition on the day of sampling, does not diagnose illness and does not replace a vet.
How does one dog’s microbiome differ from another’s?
A dog’s gut microbiome is the community of bacteria and other microorganisms that live in a dog’s gut and take part in digestion. Every dog has its own composition, but it shares part of the community with other dogs.
A 2026 study followed 35 healthy dogs whose owners collected a stool sample roughly once a month over one to two years. About 39% of the differences between samples could be explained by which dog it was (Rojas et al., 2026). So a dog has its own recognisable “signature”. It is not fixed, though: the microbiome of 34 of the 35 dogs fluctuated over time, even though the dogs were healthy the whole time.
- 39%of the differences between stool samples of 35 healthy dogs could be explained by which dog it was.Rojas et al., 2026
- 240 speciesmake up the shared core that, in an independent dataset, accounted for more than 80% of the dog gut microbiome.Castillo-Fernandez et al., 2026
- up to 95%of the DNA from dog stool could be assigned to bacteria with the new catalogue, versus only about 25% with public databases.Castillo-Fernandez et al., 2026
- 922 dogswere in the American study that examined the influence of age and lifestyle in dogs from 8 months to 18 years.Bamberger et al., 2026
How well does science know dog gut bacteria?
Until recently, using public databases of bacterial genomes, scientists could assign to a known bacterium only about a quarter of the DNA from dog stool. The rest belonged to bacteria that nobody could name. Differences between dogs were therefore measured only approximately.
In January 2026 a new canine catalogue was published in the journal Microbiome. The authors sequenced DNA from 501 stool samples from 107 healthy dogs from the USA and Europe and found 89 previously unknown species and 10 new genera of bacteria. As a result, the share of assigned DNA rose to as much as 95% from the earlier roughly 25% (Castillo-Fernandez et al., 2026). So the dog gut is not a scaled-down version of the human one. We have simply been looking at it through a human lens for a long time.
What shapes a dog’s microbiome?
The composition of a dog’s microbiome is shaped by age, diet, origin, environment and medication. The individual factors are not documented equally well, which is why the table is divided by strength of evidence.
| Factor | What the study in dogs showed | Strength of evidence |
|---|---|---|
| Diet | Two foods with different shares of protein and carbohydrate changed the composition of the microbiome in 64 dogs of two breeds within 4 weeks, regardless of breed and sex (Coelho et al., 2018) | Good (randomly assigned groups) |
| Medication | In a study of 24 healthy dogs, 16 of them received the antibiotic metronidazole for 14 days. The composition of the microbiome changed and had not fully returned even 4 weeks after stopping (Pilla et al., 2020) | Moderate (a small controlled study without random assignment) |
| Age | In 922 dogs, diversity fell with age and dogs were less similar to each other (Bamberger et al., 2026) | Moderate (different dogs at one point in time) |
| Origin and litter | Siblings from one litter had a more similar microbiome than unrelated dogs, most markedly at 7 weeks, when they were still living together (Vilson et al., 2018) | Moderate (one breed, 168 dogs) |
| Place of residence | Dogs from big cities had higher diversity than dogs from the countryside (Vilson et al., 2018) | Weaker (one breed, reason unknown) |
| Time and season | The microbiome of healthy dogs fluctuates over time, and some bacteria have seasonal swings (Rojas et al., 2026) | Moderate (35 dogs) |
One practical thing follows from the table: two dogs can react differently to the same food or treat, and one possible reason is a different microbiome. But if problems last or keep coming back, talk to your vet. You can find out how to handle a change of food gently in the article Switching dog food: a 7 to 10 day plan, and the effect of treatment on the gut is covered in the article Dog after antibiotics: how to support your dog’s tummy.
How does the microbiome change from puppy to senior?
A dog’s microbiome changes with age: in a puppy it develops quickly, in an adult it keeps fluctuating, and in older dogs it is less diverse and more individual. Studies of all three periods show this, but each has different limitations.
- Puppy. A 2022 review describes how the composition of gut bacteria changes quickly in early development and important bacteria colonise the gut gradually until the puppy grows up (Garrigues et al., 2022). In a study of 168 German Shepherds, a 7-week-old puppy resembled its mother more than an unrelated bitch (when compared with samples from the bitches 7 weeks after birth, not at birth), and siblings from one litter were more similar than unrelated dogs. Between 7 weeks and 15 to 18 months, diversity and composition kept changing (Vilson et al., 2018).
- Adult dog. Even in an adult dog the composition does not stand still. In 35 healthy dogs it fluctuated from month to month, and some bacteria had seasonal patterns (Rojas et al., 2026). In the American study of dogs aged from 8 months to 18 years, the composition gradually shifted with increasing age (Bamberger et al., 2026).
- Senior. With rising age, bacterial diversity fell and a dog’s microbiome differed more from those of other dogs (Bamberger et al., 2026). An older Japanese study, which grew the bacteria in the laboratory, found that the number and occurrence of lactobacilli tended to fall with age (Masuoka et al., 2017).
What does this mean for your dog?
The fact that every microbiome is different mainly calls for patience: there is no point measuring your dog against somebody else’s, and changes should be made slowly. Try these four steps.
- Do not compare. What works for the dog down the road may not work for yours. A difference does not have to mean you are doing something wrong.
- Change gradually. Introduce new food and treats in stages, so that the gut has time to adapt.
- Write things down. A short diary of poop, feeding and treats will show you after a few weeks what your dog reacts to. You can find out how to read poop in the article Dog poop: what colour, shape and consistency reveal.
- Allow for age. When your dog moves from puppy to adult and later to senior, talk to your vet about feeding and what to watch for.
What does science still not know about the dog microbiome?
Science cannot yet say what composition is right for a particular dog. We know that dogs differ, but not which differences are healthy variation and which are a warning signal.
- What is “normal” for one dog. Studies compare groups of dogs. There is no clear threshold for an individual dog.
- Why dogs differ. In studies, age, diet or place of residence are linked to the microbiome, but often the cause is not determined.
- Whether choosing probiotics by composition works better. Higher effectiveness of probiotics chosen according to the microbiome over ordinary probiotics has not yet been reliably shown.
Frequently asked questions
Does every dog have a different microbiome?
Yes, every dog has a slightly different composition of gut bacteria, but it shares part of the community with other dogs. In a study of 35 healthy dogs, the individual dog accounted for 39% of the differences between samples (Rojas et al., 2026). The microbiome of one dog also changes over time.
Do siblings from one litter have the same microbiome?
No, only a more similar one. In a study of 168 German Shepherds from 30 litters, siblings from one litter had a more similar composition of bacteria in the stool than unrelated dogs, but it was not identical. They were most similar at 7 weeks, when they were still living together. Changes also occurred between 7 weeks and 15 to 18 months of life (Vilson et al., 2018).
Does a dog’s microbiome change with age?
Yes. In a study of 922 dogs from 8 months to 18 years, bacterial diversity fell with age and dogs were less similar to each other (Bamberger et al., 2026). But the study compared different dogs at one point in time, not the same dogs over the whole of their lives.
Can diet change a dog’s microbiome?
Yes. In a study of 64 dogs of two breeds, two foods with different shares of protein and carbohydrate changed the composition of the microbiome within 4 weeks, regardless of breed or sex. In overweight dogs, the changes after the high-protein food were larger (Coelho et al., 2018).
Is a dog’s microbiome the same as a human’s?
No. A dog’s microbiome resembles a human’s more than a pig’s or a mouse’s (Coelho et al., 2018), but it is distinct. The new 2026 catalogue described 89 previously unknown species of bacteria from dog guts and raised the share of assigned DNA from about 25% to as much as 95% (Castillo-Fernandez et al., 2026).
Can my dog’s microbiome be measured?
Yes, from a sample of fresh stool. A laboratory describes which bacteria live in the gut on the day of sampling. Because the microbiome of a healthy dog fluctuates over time, a single analysis captures only one moment (Rojas et al., 2026). The result does not establish a diagnosis and does not replace a vet. It is a basis for a conversation with your vet.
Sources
- Rojas CA et al. (2026). Temporal variability is an inherent feature of the healthy canine microbiome assessed by full-length 16S rRNA gene sequencing. Animal Microbiome. doi.org/10.1186/s42523-026-00546-9
- Castillo-Fernandez J et al. (2026). Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery. Microbiome. doi.org/10.1186/s40168-025-02265-w
- Bamberger T et al. (2026). Mapping the canine gut microbiome: insights from the Dog Aging Project. Nature Communications. doi.org/10.1038/s41467-026-73193-y
- Vilson Å et al. (2018). Disentangling factors that shape the gut microbiota in German Shepherd dogs. PLOS ONE. doi.org/10.1371/journal.pone.0193507
- Garrigues Q et al. (2022). Gut microbiota development in the growing dog: A dynamic process influenced by maternal, environmental and host factors. Frontiers in Veterinary Science. doi.org/10.3389/fvets.2022.964649
- Masuoka H et al. (2017). Transition of the intestinal microbiota of dogs with age. Bioscience of Microbiota, Food and Health. doi.org/10.12938/bmfh.bmfh-2016-021
- Coelho LP et al. (2018). Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome. doi.org/10.1186/s40168-018-0450-3
- Pilla R et al. (2020). Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. Journal of Veterinary Internal Medicine. doi.org/10.1111/jvim.15871
This article is educational and does not replace a veterinary examination. If you are not sure, ask your vet.
This article was proofread with the help of AI. This is a translation from Czech, so it may contain inaccuracies.