Dog microbiome analysis: what the results show and don’t

A microbiome test for your dog is now available to almost anyone: you send in a stool sample and a few weeks later you get a report full of Latin names. Before you go ahead, it is worth knowing what you can read from it and, just as importantly, what the analysis cannot do.

What the analysis shows

A stool analysis describes the make-up of your dog’s gut bacteria on the day of collection. It is a useful starting point for a conversation with your vet.

1. Who lives in the gut. Which bacteria are in the gut, how varied their community is and what they might be able to do.
2. A shift from the usual make-up. This is called dysbiosis. Vets use, for example, the Dysbiosis Index, which measures the total amount of bacteria and 7 key groups and compares them with values from healthy dogs.
3. How the microbiome changes over time. Repeated measurements show how things develop, for example after a change of food or after treatment.

What the analysis does not show

• A diagnosis. Dysbiosis is a clue, not a disease. Similar changes can have several causes.
• A replacement for your vet. The result only makes sense when interpreted together with symptoms and other tests.
• Parasites. A microbiome test is not designed to look for parasites. Eggs and cysts are checked by a stool examination, and for Giardia also by a test on a stool sample (Merck Veterinary Manual).
• Easy comparison between laboratories. Sequencing methods are not yet standardised, so the results of two different laboratories cannot be compared easily.

Which methods do laboratories use?

Laboratories most often analyse dog stool in three ways: 16S rRNA gene sequencing, shotgun metagenomics and quantitative PCR (qPCR) with the Dysbiosis Index. They differ in how deeply they look and in what they compare the result with.

16S rRNA sequencing reads just one gene that all bacteria share, a sort of “name on the doorbell”. Shotgun metagenomics reads all the DNA in the sample. qPCR does not look for every bacterium; it only counts pre-selected groups.

According to an overview of canine microbiome analysis, the methods differ in what they are able to capture (Suchodolski, 2021). Similarly, in chicken gut samples (the data are not from dogs), 16S sequencing captured only part of the community that shotgun metagenomics revealed, mainly among the less abundant bacteria (Durazzi et al., 2021). The Dysbiosis Index, by contrast, has been validated directly in dogs: in a study using samples from 95 healthy dogs and 106 dogs with chronic inflammatory bowel disease, it correctly identified 95% of the healthy dogs and 74% of the sick ones (AlShawaqfeh et al., 2017).

What do the terms in the result mean?

A laboratory report usually contains diversity, relative abundance and an assessment of dysbiosis. Each of these terms means something different, and a number without context tells you nothing.

• Diversity says how many different bacteria live in the gut and how evenly they are represented. A higher number does not in itself mean better health. In healthy dogs, the richness of gut bacteria fell markedly after 14 days of metronidazole (an antibiotic) (Pilla et al., 2020).
• Relative abundance is the share one bacterium makes up of the total, for example 12%. It does not tell you exactly how many bacteria are in the gut, only how big a slice of the whole they form. When one group grows, the share of the others automatically falls.
• Dysbiosis is an imbalance of gut bacteria in which the make-up or function of the community changes compared with healthy dogs (Suchodolski, 2021). It describes a state. It is not a diagnosis and not proof of disease.
• The Dysbiosis Index sums up the qPCR result in one number: a negative value means the usual make-up, a positive one dysbiosis (AlShawaqfeh et al., 2017).

When a test makes sense

• Digestive problems keep coming back. The stool is repeatedly soft and you are already looking for the cause with your vet. The result gives your vet another piece of information. You will find more in the articles Dog poop: what colour, shape and consistency reveal and Soft stool in dogs: causes and what to do.
• After antibiotics. You want to know how the gut is recovering after treatment. See Dog after antibiotics: how to support your dog’s tummy.
• A change of food. Repeated measurements show how the microbiome develops after a change of diet. See Switching dog food: a 7 to 10 day plan.
• Choosing probiotics. You want to choose based on data, not on what happens to be on offer. See Probiotics for dogs: what they are and how to choose.

How do you choose a dog microbiome test?

When choosing a dog microbiome test, check the method, what the laboratory compares the result with, what the report contains, who explains it to you, how sampling and shipping work, and whether the test claims a diagnosis. Look for the answers before ordering, not after.

You can see what sampling, the result and the explanation look like with us on the Dog microbiome test page. Here you mostly get a guide to comparing similar offers on your own.

How do you prepare for collecting the sample?

Before collecting, write down what your dog takes and eats, and follow the laboratory’s instructions exactly. Antibiotics, probiotics and a change of food can all shift the result, so tell both the laboratory and your vet about them.

1. Note down medicines. Antibiotics can change gut bacteria for a longer time: in healthy dogs after 14 days of metronidazole, the changes were not completely resolved even four weeks after stopping (Pilla et al., 2020). Note the name of the medicine and when your dog finished it.
2. Note down probiotics and other supplements. Do not just stop them without advice. Whether to leave them out before collection is for the laboratory and your vet to decide, based on what exactly you are trying to find out.
3. Note down any change of food. In one study, when healthy dogs were gradually switched from dry food to a diet high in cooked beef, the make-up of the bacteria in the stool changed, and after the return to kibble it largely went back to its original state (Herstad et al., 2017). If the food has changed in recent weeks, say so.
4. Collect a fresh sample. Collect it at home using the collection kit, following the instructions exactly, and send it to the laboratory.

The exact requirements differ between laboratories, so the instructions on the pack always take priority over general advice.

Why is one result not enough?

The microbiome of a healthy dog naturally changes over time, so a single measurement shows just one day. Only repeating the test in the same laboratory shows whether it is a lasting deviation or ordinary fluctuation.

A study of 35 healthy dogs, whose stool was collected every month for one to two years, showed that each dog kept its own typical profile, but its microbiome fluctuated markedly over time. Some bacteria, such as Escherichia coli, were among the most variable, while others, such as Peptacetobacter hiranonis, were more stable (Rojas et al., 2026).

• Measure in the same laboratory. Otherwise you are comparing two different methods, not two states of the gut.
• Read the trend, not one number. The direction of change matters more than a small deviation.

What does working with your vet on the result look like?

Bring the result to your vet together with what you have noticed in your dog, because they only make sense together. The laboratory describes the bacteria, and your vet assesses your dog and decides on the next steps.

1. Bring the paperwork. The laboratory report, a list of medicines and supplements, details of the food and a short record of stools and appetite.
2. Ask about connections. What in the report corresponds to your dog’s problems, and what is just a deviation?
3. Agree on the next step. Your vet may recommend further tests, an adjustment of the food or a follow-up sample.
4. Choose probiotics based on data. If your vet recommends probiotics, the result can serve as a basis for choosing instead of guesswork. But studies showing in dogs that choosing based on an analysis works better are still missing.

What to ask the laboratory

• Which method will it use to analyse the sample?
• What does it compare the result with, that is, with which values from healthy dogs?
• How long do results take, and who will interpret them?
• What should I tell the laboratory before collection (medicines, food, supplements)?

A good laboratory will be happy to explain this to you. To find out what the dog microbiome is, read the article Dog gut microbiome: what it is and why it matters.

Sources

1. Suchodolski JS (2021). Analysis of the gut microbiome in dogs and cats. Veterinary Clinical Pathology. doi.org/10.1111/vcp.13031
2. AlShawaqfeh MK et al. (2017). A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy. FEMS Microbiology Ecology. doi.org/10.1093/femsec/fix136
3. Herstad KMV et al. (2017). A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs. BMC Veterinary Research. doi.org/10.1186/s12917-017-1073-9
4. 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
5. Durazzi F et al. (2021). Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota. Scientific Reports. doi.org/10.1038/s41598-021-82726-y
6. 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
7. Merck Veterinary Manual. Diagnostic Procedures for the Private Practice Laboratory: Parasitology (stool examination, Giardia, repeat testing). merckvetmanual.com