Your dog’s microbiome

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

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 illness 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.

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 result from antibiotic use, may 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.

Further research shows that a high-fat diet exacerbates the problem, and that changes in the metabolic pathways remain throughout life.

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 antibiotics are necessary, do damage control by providing your pet with foods and supplements that nourish gut flora.

Here’s what you can consider:

  • Fermented vegetables – they help feed his gut microbiome.
  • High quality probiotic supplements – they restore the microbiome after drug therapy or during times of stress.
  • Digestive enzymes – to promote healthy digestion. Look for animal-derived supplements that ideally contain some or all of these ingredients: betaine HCI, ox bile extract, bromelain, papain, pancreatin, protease, amylase and lipase.

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.



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Dr. Karen Becker is a holistic veterinarian and wildlife rehabilitator. She has certification in acupuncture and homeopathy and in 1999 opened the Natural Pet Animal Hospital in Tinley Park, Illinois. Dr. Becker is also a licensed Naturopathic Medical Doctor.