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Gut Health For Dogs: A Veterinarian’s Guide

Dr. Julie Buzby April 27, 2026

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Gut health for dogs affects not only digestion but also the immune system and temperament, and plays a role in some diseases. But what impacts gut health, and how do you know if your dog has good gut health? What can do you to improve your dog’s gut health? That’s exactly what integrative veterinarian Dr. Julie Buzby is about to explain.

Dog staring at a bowl of food

From a veterinary perspective, we know that a healthy dog truly begins with a healthy gut. While many factors contribute to a dog’s well-being, digestive health plays a foundational role. It influences everything from nutrient absorption to immune function. In many ways, gut health helps set the tone for the entire body.

What is gut health and why is it important for dogs?

Gut health is a measure of how well the digestive system is functioning overall. It looks at the way the organs, tissues, cells, microbes, and molecules that make up the gut are working together to accomplish their specific function and to contribute to the overall health and well-being of the dog.

Understandably, it is easy to think about gut health in terms of the digestion of food, absorption of vital nutrients, and elimination of waste products from the body. And you would be right to do that.

Imbalances in gut health most commonly show up as digestive upset—nausea, vomiting, diarrhea, constipation, and flatulence. And poor digestive health can cause weight loss or weight gain, depending on the underlying imbalance.

But as veterinarians have discovered, this is just the tip of the iceberg.

The gut plays a huge role in the immune system. In fact, 70-80% of the immune system is located in the digestive tract. Thus, poor gut health can interfere with the normal function of a dog’s immune system, increasing his or her susceptibility to disease.

Gut health imbalances have also been linked to allergies, kidney and liver disease, and arthritis. And more recent studies have uncovered a connection between poor gut health and behavioral changes like anxiety and aggression.

How does the gut microbiome contribute to gut health in dogs?

One of the big players in gut health is the millions of different microscopic organisms in the digestive tract, known as the gut microbiome. It includes more than 1,000 species of beneficial bacteria, as well as viruses, protozoa, single-celled organisms called archaea, and even some fungal species.

Together, these microorganisms help digest food, support the immune system, produce vitamins, and absorb nutrients.

Factors influencing the microbiome

Many factors can influence the balance of the microbiome.

Diet

This is one of the biggest factors. The levels of fiber, protein, and carbohydrates in the dog’s diet, as well as the form of the diet (raw versus canned versus dry), may impact the microbial populations.

Stress

Short-lived stress (boarding, visitors, etc.) can temporarily alter the microbiome. And more prolonged stress is linked to decreased numbers of “good” bacteria and overgrowth of “bad” bacteria.

Size of dog

Larger dogs have a longer gastrointestinal tract. This may allow for improved digestion and GI conditions that are optimal to block the growth of some “bad” bacteria. Thus, larger dogs may have better gut health than smaller ones.

Breed of dog

Interestingly, even in dogs of a similar size, the gut microbiome varies from one breed to another.

Antibiotic use

Being on antibiotics for an infection may temporarily kill off some of the “good” bacteria, allowing more “bad” bacteria to start multiplying. One study indicated this effect may persist for four to six weeks.

Owner giving a dog an antibiotic, which may upset gut health
Antibiotics have the potential to kill off good bacteria in your dog’s gut.

Age

Diversity of the microbiome increases as the dog approaches adulthood. But then it tends to decrease again as the dog becomes a senior. This may cause senior dogs to have less efficient digestion, poorer immune function, and a higher chance of harmful bacterial growth in the gut.

Where the dog grew up

Dogs raised in a house versus a kennel may have different gut microbiomes. However, this link is not as clear-cut, since diet and other factors may contribute to the differences as well.

How do I know if my dog’s gut is healthy?

If the dog has a well-balanced microbial population in the gut, this is called eubiosis. In this state, he or she shouldn’t be showing signs of digestive upset like nausea or vomiting. Stool consistency should be normal, and bowel movement frequency should be regular each day.

Furthermore, dogs in eubiosis typically have shiny, healthy coats and skin that is not itchy, scabbed, or inflamed. And behaviorally, one might expect a dog in eubiosis to have a stable temperament, rather than show signs of anxiety or aggression.

What are the symptoms of poor gut health in dogs?

In a dog whose microbiome is unbalanced, or in a state of dysbiosis, the populations of good gut bacteria may start to shift. This allows bad bacteria to flourish, disrupting a dog’s gut and increasing the likelihood that digestive issues or other problems may develop.

The symptoms that a dog with poor gut health may experience can vary widely. Some symptoms appear quickly, whereas others develop over time in the face of a chronic state of dysbiosis. 

Symptoms of poor gut health in dogs may include:

  • Lethargy: Being a lethargic dog is possible if your dog isn’t getting the energy from food that he or she needs or is generally feeling unwell.
  • Loss of appetite: A disrupted gut may lead to a dog who doesn’t feel like eating.
  • Nausea: The dog may keep licking the lips, lick the floor or furniture, or drool excessively.
  • Vomiting: Sometimes, dogs may vomit intermittently.
  • Diarrhea: The diarrhea might be soft stool, or it might be loose and watery. And you could see dog diarrhea with blood or mucus in it.
  • Constipation: Straining to defecate and/or having less frequent bowel movements that consist of hard, dry stool may occur due to constipation in dogs.
  • Increased gas: You might hear your dog’s stomach rumbling, or he or she may pass gas more frequently.
  • Abdominal distention: While not life-threatening like gastric dilatation and volvulus (GDV in dogs), sometimes dysbiosis can lead to mild bloating. This can cause abdominal pain. As a result, you may see your dog in the play bow position in an attempt to get comfortable.
  • Weight loss: Due to the malabsorption of essential nutrients from the dog’s diet, the dog may lose weight.

What health conditions are linked to poor gut health in dogs?

In addition to the symptoms above, sometimes a dog will suffer from a health issue that is linked to poor gut health. The poor gut health may have contributed to the condition, or the condition may have led to poor gut health.

Inflammatory bowel disease (IBD)

Dogs who suffer from inflammatory bowel disease (IBD in dogs) tend to have reduced diversity of microbial species in their gut microbiome. This leaves the dog with fewer “good” bacteria that can break down fiber and carbohydrates in the diet to produce short-chain fatty acids (SCFAs).

Normally, SCFAs help keep the pH of the gut low to block disease-causing organisms from growing. Plus, they assist with energy metabolism and help protect the lining of the intestines. Reduced amount of SCFAs in dogs with IBD makes the lining of the intestines more susceptible to inflammation and injury. This triggers the immune response and perpetuates a vicious cycle of chronic inflammation.

Stress colitis

As discussed earlier, stress (especially the stress hormone cortisol) can lead to dysbiosis. Plus, it disrupts the lining of the intestine, which allows bacteria and toxins from the gut to leak into the bloodstream. This leads to inflammation. Finally, stress causes food to move through the digestive system more quickly. Since food spends less time in the GI tract, where water and nutrient absorption occur, the stool ends up being looser.

All these changes together may contribute to stress colitis in dogs—inflammation of the colon that typically shows up as diarrhea (which may contain blood or mucous) after a stressful event.

Exocrine pancreatic insufficiency (EPI) in dogs

In exocrine pancreatic insufficiency (EPI in dogs), the pancreas doesn’t produce enough digestive enzymes. As a result, fats and proteins in the diet aren’t properly digested and absorbed. This upsets the balance of good bacteria in the gut and can contribute to the onset of another condition called small intestinal bacterial overgrowth (SIBO). This further interferes with proper nutrient absorption.

German Shepherd dog laying down in the grass
EPI can lead to the disruption of the balance of good vs. bad bacteria in your dog’s gut.

Allergies and other skin problems

In recent years, veterinary researchers have identified a connection between gastrointestinal health and skin disease called the gut-skin axis. Research is ongoing, but it appears that gut health plays a role in the development of dog seasonal allergies (atopic dermatitis) and potentially other skin conditions, too.

Researchers have proposed that an imbalance of good versus bad microbial species present in the gut at any given time may be one of the factors that contribute to atopic dermatitis. Interestingly, there appears to be a similar link between dysbiosis, damage to the intestinal barrier, and atopic dermatitis (eczema) in humans.

Behavioral disorders (anxiety and aggression)

Along the same lines, the gut and brain also communicate back and forth with one another. This is called the gut-brain axis, and it explains the potential link between canine behavioral disorders and the gut microbiome.

Research has demonstrated that the microbial population in the gut has an impact on the levels of many brain-signaling chemicals (neurotransmitters), including serotonin, GABA, and dopamine. These molecules help regulate mood, sleep, memory, motivation, social interactions, and anxiety. Altered levels of neurotransmitters, as seen in some dogs with poor gut health, may make dogs more prone to anxiety or aggression.

Additionally, short-chain fatty acids (SCFAs) produced by a healthy gut may support brain function. As a result of reduced SCFAs, dogs with poor gut health could potentially have more memory or stress problems.

Additional diseases

In addition to the conditions discussed above, studies have indicated that higher levels of dysbiosis may also be present in:

  • Liver disease in dogs
  • Kidney failure in dogs
  • Respiratory infections
  • Diabetes in dogs
  • Osteoarthritis in dogs
  • Mitral valve disease in dogs.

It will be interesting to see what new discoveries scientists make in the coming years regarding the interconnection of gut health and overall health.

How will the vet diagnose gut health disorders?

If your dog is experiencing changes in his or her gastrointestinal health and comfort, scheduling a visit with your veterinarian is the best first step to identifying the underlying cause(s). While it would be handy, there isn’t a simple, clinically available test to rate a dog’s gut health.

Instead, the vet will infer gut health status based on the data he or she collects during the exam and testing. Plus, he or she will search for the underlying cause of the dysbiosis.

Initially, your vet will start by reviewing your dog’s medical history. You should bring a list of your dog’s diet, treats, medications, flavored chews, and supplements. And make notes of any unusual symptoms you’ve observed at home, too. 

Then your vet will conduct a thorough physical examination to evaluate your dog from nose to tail. He or she will palpate the abdomen for pain, masses, or other abnormalities (gassy-feeling intestines, hard stool, etc.). Plus, the vet will carefully look at the skin and coat and evaluate the rest of the body systems.

Running laboratory tests

Next, the vet might recommend some basic diagnostic tests including:

  • Fecal examination: Fecal tests for dogs can help identify parasites, bacteria (like Clostridium), or yeast, which can cause digestive upset and fecal abnormalities. The veterinary team can collect a fecal sample during your dog’s appointment, or you can bring a fresh sample with you.
  • Fecal culture or other specialized fecal tests: The vet may recommend additional fecal tests if the routine fecal samples are negative for parasites. These special tests may also be helpful if your dog has been treated repeatedly for abnormal stools with no improvement.
  • Blood and urine samples: Baseline blood tests for dogs typically include a CBC (complete blood count) and chemistry panel. Plus, the vet might recommend a urinalysis. These tests provide an overview of your dog’s health and help screen for some common diseases.
Vet examining a dog with poor gut health
Your vet may recommend diagnostic tests to determine the cause of your dog’s poor gut health.

Performing imaging, endoscopy, or colonoscopy

If the vet feels it is warranted based on the history, physical, and baseline tests, he or she may also recommend imaging.

X-rays of the abdomen, sometimes with a contrast medium like barium to highlight abnormal areas along the digestive tract, can be a good place to start. Additionally, the vet may perform an abdominal ultrasound to help identify specific abnormalities in the stomach, intestines, or other organs.

In some cases, endoscopy or colonoscopy is necessary to evaluate the interior of the stomach, intestines, or colon. At the same time, the vet may collect biopsy samples from those regions and send them to a veterinary pathologist for further microscopic evaluation.

Reaching a diagnosis

Finally, the vet will interpret the information. He or she probably isn’t going to diagnose your dog with “poor gut health” per se. Rather, the diagnosis will likely be the contributor to the poor gut health—IBD, stress colitis, whipworms, dietary indiscretion, systemic disease, etc.

How can you improve poor gut health?

If your dog is suffering from poor gut health and associated conditions, the goals are to:

  1. Improve the microbiome using prebiotics, probiotics, postbiotics, fecal microbiota transplantation, and/or special diets that promote good gut health.
  2. Address whatever health condition or situation led to the dysbiosis in the first place (if possible).

Prebiotics to improve gut health in dogs

Prebiotics are non-digestible, fiber-based components found in many foods. They support the growth of good gut bacteria to help stabilize the gut microbiome. Think about them sort of like the food for the gut bacteria.

Human prebiotic foods that are safe options for dogs in moderation include:

  • Oats: Generally rolled oats cooked into oatmeal using water instead of milk (avoid instant oatmeal due to the sugar and flavorings).
  • Canned pumpkin for dogs: Don’t use pumpkin pie filling, which may contain spices or xylitol (birch sugar), which is toxic to dogs.
  • Flaxseed: Add a small amount of chopped or ground seeds to your dog’s food.
  • Bananas: Peel them first and stick to using them as an occasional treat since they are higher in sugar.
  • Apples: Cut into slices or pieces with the seeds, core, and stem removed. (Whole apples or large pieces can pose a choking hazard.)
  • Chicory root: Available as a powder or as an ingredient in dog foods and supplements.
  • Medicinal mushrooms like turkey tail, shiitake, and maitake: Cooked or as a supplement containing the whole mushroom. (Don’t feed your dog wild mushrooms as misidentifying them can be dangerous.)
  • Sweet potatoes: Can be cut into small cubes and fed raw (beware of choking), baked, or mashed.

Note: Too much prebiotic fiber at once can lead to diarrhea, gas, or bloating. Starting slowly and feeding these foods in reasonable amounts is important.

Additionally, there are dog-specific supplements available that combine prebiotics and probiotics. This is convenient because it is a ready-made source of the good gut bacteria and their food.

Probiotics

Probiotics for dogs are live bacterial cultures that play a role in protecting intestinal health. Their benefits include:

  • Blocking harmful bacteria and other pathogens from attaching to the gut wall
  • Supporting the integrity of the intestinal mucosal barrier
  • Aiding immune function and inhibiting the release of pro-inflammatory molecules (cytokines)
  • Assisting in the production of vitamins (B and K), serotonin (the “feel good” hormone), and several enzymes
  • Optimizing the balance of organisms in the gut microbiome

As you can see, probiotics are key to protecting the health of a dog’s gut. They are beneficial in many conditions, including IBD, pancreatitis in dogs, bacterial overgrowth in the small intestine, diarrhea, yeast infections, urinary tract infections (UTI in dogs), and even anxiety and obesity. 

Dog eating food with probiotics to help improve his gut health
Probiotics can help improve your dog’s gut health.

Many dog parents choose to purchase a dog-specific, commercially available probiotic supplement. This is generally the most effective way to supply a large number of beneficial organisms to your dog.

However, some human foods are also safe probiotic options for dogs to enjoy in moderation. The list includes low-fat, plain unsweetened yogurt for dogs (not sugar-free due to the risk of xylitol toxicity), plain unsweetened kefir, fermented fruits (blueberries), and fermented vegetables (carrots or broccoli).

Before feeding fermented fruits or vegetables, check with your vet, as they are not suitable for all dogs. And keep in mind that some dogs don’t digest lactose well. Kefir is lower in lactose than yogurt but could still cause some GI upset.

Postbiotics

Postbiotics, as defined by the International Scientific Association of Probiotics and Prebiotics in 2021, are “a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host.” In other words, they are a supplement designed to replicate the substances (compounds and dead microbes) normally produced by a healthy gut microbiome.

Postbiotics may include short-chain fatty acids (like butyrate), other acids, various enzymes, cell wall fragments, and antimicrobial compounds. These components provide energy for cells, help reduce inflammation, have antimicrobial effects, promote gut health and barrier function, act as antioxidants, and support immune system function.

There are a variety of commercially available postbiotic supplements for dogs, and some dog foods also contain postbiotics.

Dog foods for good gut health

If your vet suspects that your dog has a gut health disorder, he or she may recommend a specialized diet to help regulate the gastrointestinal biome and manage any underlying conditions. This might be a prescription diet suited to your dog’s situation, an over-the-counter (OTC) diet with gut benefits, or a bland diet for dogs.

If your vet recommends a prescription diet, it is for good reason. Yes, these diets do tend to cost more, which can be stressful when you are already spending money on office visits, diagnostic tests, and medications.

But prescription diets may work better than OTC diets because they are tailored to support the dietary needs of dogs with specific conditions. And they are typically manufactured and packaged in separate, dedicated production lines or facilities to avoid cross-contamination, whereas OTC diets are not. 

Fecal microbiota transplantation (FMT)

The process of fecal microbiota transplantation (FMT) involves transferring fecal matter from a healthy donor dog to a sick dog. Veterinarians introduce the fecal material either via enema, endoscopy, or as an oral capsule of freeze-dried fecal matter that the dog swallows. 

Dogs diagnosed with acute diseases, like parvovirus, or chronic disorders like IBD, have benefited from FMT in clinical practice. Interestingly, research into the benefits of FMT for disorders like canine cognitive dysfunction (CCD), seizures in dogs, anxiety, aggression, and environmental allergies (atopic dermatitis) shows promising results, too.

Condition-specific treatments

Additionally, the vet will prescribe treatments to manage any concurrent conditions your dog is dealing with. This might be digestive enzymes for a dog with EPI or immunosuppressants to address IBD. Or it could be allergy medications for dogs with seasonal allergies.

The list of conditions linked to poor gut health is long, so it isn’t possible to address them all here. However, keep in mind that if your dog needs antibiotics as part of the treatment plan, it will be particularly important to use pre-, pro-, and postbiotic supplements to help restore balance in the gut.

How can I keep my dog’s gut healthy?

If your dog has experienced a gut health disorder, your primary focus moving forward is likely how to improve his or her gut health to avoid further issues. The following strategies may be helpful:

1. Partner with your veterinarian.

Working with your veterinarian is the first line of defense in helping your dog avoid future episodes of dysbiosis. This may involve scheduling regular wellness exams for your dog and performing recommended screening tests such as fecal tests or bloodwork.

Additionally, it is important to let your vet know when you notice changes in your dog’s appetite, stool quality, energy level, appearance, or behavior. These could be early indicators of dysbiosis or another medical problem.

2. Feed your dog a balanced diet.

The diet you choose for your dog should be appropriate for his or her age, lifestyle, and health history. This includes feeding prescription diets to address specific conditions as recommended by your vet.

3. Work with the vet to develop a parasite prevention program.

Keeping your dog on year-round heartworm, flea, and tick prevention can go a long way in preventing several serious diseases. If you haven’t already, it is a great idea to speak with your vet about the prescription option that will be the best fit for your dog’s lifestyle. (OTC parasite preventives may be ineffective or even unsafe.)

4. Limit how many treats your dog gets.

As a general rule, treats should make up less than 10% of your dog’s daily total caloric intake. More than this could lead to weight gain and potentially suboptimal gut health.

If your dog is on a prescription diet, ask your veterinarian which treats are okay for your dog to have. Several companies, like Hill’s, Purina, and Royal Canin, do offer treats that specifically complement several of their prescription diet lines.

5. Avoid giving your dog table scraps.

It can be tempting to offer your beloved dog a little nibble of food from your dinner plate. But human foods can be problematic for dogs to digest. Many human foods are too high in fat and sugar to be digested by a dog without causing some level of gastrointestinal distress. Plus, calories from table food can be hard to quantify. Thus, they can easily sneak up on your dog in the form of a few extra pounds.

6. Partner with a veterinary nutritionist.

If your dog has specific dietary needs, ask your vet about consulting with a veterinary nutritionist. This customized service can be especially helpful for dog parents who prefer to home-cook for their dog. A veterinary nutritionist will be able to help you build a balanced, healthy diet tailored specifically for your dog. And he or she can also guide you on ingredients to avoid based on your dog’s health history and diagnosis.

7. Slowly transition your dog from one food to another.

For any dog, it’s critical to transition slowly from an old diet to a new one. Slow transitions allow your dog’s digestive tract to acclimate to the ingredient profile of the new diet. This avoids or minimizes digestive upset like nausea, vomiting, diarrhea, or excessive gas.

Note: Bland diets are an exception, as the vet may have you start feeding only that food right away. Otherwise, remember to slowly transition to all diets, whether they are OTC, prescription, or prepared at home.

8. Consider using slow-feeder bowls or automatic food dispensers.

Slowing how quickly your dog eats can help prevent digestive issues. Dogs that gulp their food too quickly often swallow extra air, which can cause gas, bloating, or regurgitation of undigested food. Similar issues can occur when dogs consume very large meals.

Using a slow feeder bowl and/or dividing your dog’s food into several smaller meals throughout the day can help minimize nausea, regurgitation, bloating, and sudden blood sugar swings. This is important since all of these symptoms can cause discomfort and contribute to additional health concerns.

A healthy gut makes a healthy dog

It’s easy to think of the gut as just part of the digestive system. But it’s actually a cornerstone of your dog’s health. As the gateway to whole-body wellness, your dog’s digestive system affects how nutrients are absorbed, how the immune system functions, and so much more.

Thus, it is important to work alongside your veterinarian to make informed choices that support your dog’s gut health—and overall health—at every stage of his or her life.

What do you do to keep your dog’s gut healthy?

Please comment below.

Filed Under: Happy, Healthy Dog Care, Our Blog: The Buzby Bark

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About Dr. Buzby

Dr. Buzby with a golden retrieverDr. Julie Buzby has been an integrative veterinarian for twenty years and has earned certification by the American Veterinary Chiropractic Association in 1998, and by the International Veterinary Acupuncture Society in 2002.
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