Your dog’s microbiome

A healthy gut equals a healthy dog. Take a close-up look at his gut microbiome, and why it’s so vital to his well-being.

By now, you’ve probably heard the term “microbiome”, although you may not know exactly what it means. The microbiome describes the collection of billions of microorganisms (microbiota) that live in and on your dog’s body (and your own). The microbiome is made up of several distinct areas, including the eyes, genitals, mouth and skin, as well as the intestines, which comprise the all-important gut microbiome. Microbiota serve many beneficial functions – they control pathogens, support gut health and the immune system, produce vitamins and short chain fatty acids, and much more. In this article, we’ll focus on the gut microbiome, and how it influences your dog’s overall health.

Why the gut microbiome is so important

Some microbes promote health while some are harmful. To describe the non-harmful relationships, researchers use the terms “commensalism” and “mutualism”. A commensal relationship means the microbe is beneficial by being in the host body, but it doesn’t affect the host. A mutual relationship means the microbe is good for the host, and the host body conditions are favorable to the microbe.

Both commensal and mutual relationships can be very useful for the host. For example, some microbes in the human gut digest vegetable fibers, and in turn, the microbes are given food and energy.

Some harmful microbes are also part of your dog’s microbiome. They can, for example, excrete metabolites that are not beneficial to the host body, or can even be pathogenic, meaning they cause illness. Salmonella is a pathogenic microbe. It can cause diarrhea in humans, but dogs very rarely get sick from it, even though they may have it in their gut quite often.

In recent years, it has become abundantly clear that the composition of microbes in the gut plays a crucial role in health and disease prevention. This makes sense because 70% to 80% of your dog’s immune system is located in the gastrointestinal tract. When we disrupt the gut microbiome, we automatically disrupt immune function, which can have far-reaching consequences.

In humans, studies have established an association between gut microbes and dozens of health conditions, including obesity, allergies, diabetes, chronic fatigue syndrome, cancer, Parkinson’s, autism, organ disease, depression and more.

Studies of dogs (and cats) suggest that many of the conditions often seen in today’s pets, such as oral disease, GI diseases such as IBD, skin and urinary tract problems, and bacterial infections, are all linked to changes in the gut microbiome.

It’s also important to realize that genetics account for only about 10% of canine illnesses. The remaining 90% have environmental causes, with the most prevalent being an inappropriate diet.

Maintaining your dog’s microbiome health

One of the most important steps you can take to keeping your dog’s microbiome healthy is to avoid antibiotic use, except when a bacterial infection has been definitively diagnosed and all other treatment options have been exhausted.

If your veterinarian recommends a course of antibiotics, insist that he or she first perform a culture and sensitivity test to identify the bacteria involved and the best drug to treat it. If your vet does not complete a culture and sensitivity test, it means he or she is guessing at what antibiotic will be necessary to cure the infection, which isn’t good medicine and certainly not good for your pet’s microbiome.

Another very important step in preserving your dog’s long-term gut health is to perform damage control in situations where the microbiome may be altered, such as in the case of antibiotic therapy for a life-threatening infection. This involves providing your pet with foods and supplements that nourish gut flora.

For the purposes of both mitigating damage and maintaining the resiliency of your dog’s gut, your best option is to feed a nutritionally-balanced, species-appropriate, non-genetically modified, fresh food diet.

Researchers in Italy conducted a study to investigate the influence of a raw pet food diet versus an extruded (dry food) diet on the microbiome of dogs. The results suggest that raw diets promote a more balanced growth of gut bacterial communities, and a positive change in healthy gut function.

  • Offering fermented vegetables to your dog is another great way to help feed his gut microbiome.
  • High quality probiotic supplements restore the microbiome after drug therapy or during times of stress.
  • Another very beneficial supplement for promoting healthy digestion in your dog is digestive enzymes. High quality digestive enzymes for pets should be animal-derived and ideally contain some or all of these ingredients: betaine HCI, ox bile extract, bromelain, papain, pancreatin, protease, amylase and lipase.

Antibiotics – one of the biggest threats to the microbiome

Antibiotics indiscriminately kill gut bacteria, both good and bad. This is why secondary infections and lowered immune function are common side effects of taking antibiotics. Chronic low-dose exposure to antibiotics through food also takes a toll on the gut microbiome, and can result in chronic ill health and increased risk of drug resistance.

Scientists who have studied the impact of early-life antibiotic therapy on body composition have proven that altered microbiota, which can be the result of antibiotics, can cause obesity through processes that create inflammation or change metabolic activity in the gut. These processes can also result in diabetes and fatty liver disease.

Research additionally suggests that antibiotics disrupt the early development of microbiota. Studies involving livestock animals that receive sub-therapeutic (low dose) levels of antibiotics to promote growth show that the earlier in life the antibiotics are given, the more profound the effect. Exposure to antibiotics in early infancy changes the composition of the animal’s microbiota, leaving it more vulnerable to disruption.

These results show a clear link between antibiotics and changes in metabolic pathways. Further research shows that a high-fat diet exacerbates the problem, and that changes in the metabolic pathways remain throughout life.

Other factors that disrupt gut bacterial balance

The bacteria in your dog’s GI tract can be influenced by a number of additional factors — everything from emotional stress to an unhealthy lifestyle. Stressors that can throw your dog’s gut bacteria out of balance include:

  • Sudden change in diet
  • Poor quality or biologically inappropriate diet
  • Pica (eating non-food items such as feces, sticks, rocks, etc.)
  • Drinking contaminated water
  • Vaccinations
  • Surgery
  • GI disease
  • Travel or boarding
  • Emotional stress (often caused by a change in routine or environment)

When physical or emotional stress upsets the bacterial balance in your dog’s gut, it can trigger a cascade of nutritional problems, including poor nutrient absorption and intermittent or chronic diarrhea. It also opens the door to leaky gut syndrome (dysbiosis), which means partially digested amino acids and allergens are able to enter the bloodstream. This in turn can create a host of other health problems, from allergies to autoimmune disease and changes in behavior.

Your dog’s gut is home to a diverse and complex community of microbiota that serve a range of important functions. Keeping his gut microbiome balanced is crucial to maintaining his overall health and helping to prevent a variety of diseases.


Veterinarian Dr. Karen Shaw Becker received her degree from the Iowa State College of Veterinary Medicine. She owns/operates Natural Pet Animal Hospital, Feathers Bird Clinic, TheraPaw Rehabilitation and Pain Management Clinic and Covenant Wildlife Rehabilitation in Illinois. She co-authored Real Food for Healthy Pets and hosts a holistic animal wellness website (