The Science / Gut Health
TopicGut Health & The Microbiome
Itching that won't quit. Ear infections that keep coming back. Loose stools nobody can solve. For many dogs and cats, the answer starts in the gut, where much of the immune system is trained.
The immune system lives where the food goes.
The lining of the intestine holds the gut-associated lymphoid tissue, or GALT. It is the largest concentration of immune tissue in the body, and it is where immune cells are produced, trained, and regulated.
Alongside it lives the microbiome: trillions of bacteria and other organisms that help digest food, produce compounds that fuel the gut lining, and keep opportunistic organisms in check. Researchers have linked changes in this community to digestive disease in dogs and cats. Integrative practitioners see the same pattern show up in the skin, the ears, and the immune system.
That is why chronic ear scratching, recurring skin infections, and loose stools so often lead back to the same conversation. Not because everything has a single cause, but because the immune system regulates so much of it.
Three pressures on the gut.
- Heavily processed food. In a large Finnish study, puppies fed a non-processed, meat-based diet early in life had fewer owner-reported allergy and atopy skin signs as adults than puppies fed an ultra-processed, carbohydrate-based diet.
- Antibiotics. They are often necessary, and they work by killing bacteria across categories. In healthy dogs given a two-week course of metronidazole, the gut microbiome shifted significantly, and in some dogs it had not fully recovered four weeks after the last dose.
- Everyday stressors. Stress, some long-term medications, and the cumulative load of daily exposures all act on the gut. Most pet parents are never told to support the gut while these are in play.
Questions and habits to bring to your vet.
- Ask about gut support with every antibiotic.
The prescription solves the infection. Ask what to do for the microbiome during the course and after it ends.
- Time probiotics around antibiotics.
A probiotic given at the same time as an antibiotic is largely wasted. Space them at least two to four hours apart.
- Look past single-strain products.
Read the label. A single strain with a flavor enhancer is not the same as a multi-strain formula with digestive enzymes.
- Add real food where you can.
Bone broth made without onion, and a few tablespoons of plain kefir, are simple additions many integrative practitioners use. Check with your vet first.
Go deeper on Integrative Pet Parent.
Why 70% of Your Dog’s Immune System Lives in Their Gut
The single most important sentence in integrative pet medicine, and what it means for the dog in front of you.
Read the articleAntibiotics and the Microbiome: What to Do During and After
Your dog needs the antibiotic. The microbiome needs you to know what comes next.
Read the articleGut
Why probiotics and digestive enzymes come first, and what to look for on the label. For dogs and cats.
Read the articleThe research behind this page.
- Pilla R, Suchodolski JS. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. Frontiers in Veterinary Science, 2020.
- Hemida M, et al. Puppyhood diet as a factor in the development of owner-reported allergy/atopy skin signs in adult dogs in Finland. Journal of Veterinary Internal Medicine, 2021.
- Pilla R, et al. Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. Journal of Veterinary Internal Medicine, 2020.
- DogRisk research group, University of Helsinki.
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Jennifer Makeeff writes Integrative Pet Parent. She has advanced education in integrative pet health and has studied alongside leading veterinarians and scientists in integrative care. She is not a veterinarian. She is a translator, a pattern reader, and an advocate for your pet. More about Jennifer.
This library is education, not veterinary advice. Work with your veterinarian before changing your pet's diet, supplements, or medications. In an emergency, go to your vet or an emergency clinic.