• ENCINITAS (760) 753-9366
  • OCEANSIDE/CARLSBAD (760) 941-3221
  • POWAY (858) 748-9676
Mutt Mail

Why Is Your Pet’s Gut Bacteria Out of Whack?

May 19, 2022 | General


  • Both physical and emotional stressors can disrupt the balance of bacteria in your pet’s GI tract; it’s important to address this issue, since the right balance is necessary for optimal digestion and immune system function
  • When good-to-bad gut bacteria is out of whack, it can result in digestive and nutritional issues, leaky gut syndrome, and ultimately, a host other health problems
  • Another major influence on gut bacterial balance in pets is the overuse of veterinary drugs, including antibiotics, steroids, flea and tick medications and nonsteroidal anti-inflammatories
  • Ensure your pet has a healthy microbiome through a nutritionally optimal, minimally processed diet that includes fermented vegetables, prebiotic-loaded low glycemic veggies and if necessary, a high-quality probiotic supplement

By Dr. Karen Shaw Becker – Read Full Article

Probiotics are the beneficial bacteria that dogs and cats need to maintain healthy levels of friendly bacteria in the gut, and to discourage potentially pathogenic bacteria from taking over.

Your pet’s digestive tract is the largest immune organ in her body, and home to an incredibly large population of organisms (including bacteria, protozoa, fungi and viruses) that make up the gut “microbiome.” The digestive tracts of canines and felines are specifically designed to handle a tremendous bacterial load from the food they consume, because in the wild, the prey they eat is pretty much the opposite of sterilized and pathogen-free!

Your pet’s gastrointestinal (GI) tract must maintain a healthy level of good bacteria and a diverse spectrum of different kinds of friendly gut organisms in order to support the immune system.

If populations of healthy gut organisms diminish or there’s not enough diversity in the microbiota (a.k.a microbiome communities — the collection of micro­organisms that live in and on the body), all sorts of GI and immune issues can develop, including an increase in the number of potentially pathogenic bacteria, which can create dysbiosis, small intestinal bacterial overgrowth (SIBO) and/or leaky gut syndrome.

Studies show animals without rich microbial diversity, adequate colonies of friendly bacteria in their gut, or who suffer from microbiome imbalances (a poor balance of good-to-bad gut bacteria) are at high risk of developing a wide range of chronic diseases.

How Your Pet's Gut Bacteria Gets Out of Whack

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

When physical or emotional stress upsets the bacterial balance in the gut, it can trigger a cascade of 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.

Antibiotics Can Lead to Obesity, Diabetes and Liver Disease

The most common veterinary-related cause of bacterial imbalances in pets is the use of drugs that disrupt the microbiome, including the perpetual use of anti-inflammatories (both steroidal and nonsteroidal), the routine application or ingestion of flea/tick pesticides and of course, overuse of antibiotics.

Laura Cox, PhD, of New York University’s Langone Medical Center, has studied the impact of early-life antibiotic therapy on body composition. According to Cox, several researchers have proved that altered microbiota which can result from antibiotic use, can cause obesity through processes that create inflamma­tion or change meta­bolic activity in the gut. These processes can result not only in obesity, but also diabetes and fatty liver disease.1

According to Cox, research suggests that antibiotics disrupt early development of microbiota. Studies involving production animals that received subtherapeutic (low dose) levels of antibiotics to promote growth show that the earlier in life the antibiotics are given, the more profound the effect.

Similar studies conducted with mice have produced an increase in fat mass. Cox’s studies have shown that exposure to antibiotics in early infancy changes the composition of the microbiota, leaving it more vulnerable to disruption. In the mice studies, the animals not only gained weight, they also accumulated more visceral and liver fat.

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

In addition to demonstrating that antibiotics early in life cause alterations in microbiota that result in changes in body composition, Cox has also proven that the microbes alone can trigger fat accumulation. In fact, germ-free mice that were administered microbiota from antibiotic-treated mice gained more weight and fat than mice that received microbiota from control mice.2

In my experience, many veterinarians are entirely too quick to prescribe antibiotics for health issues that can (and should) be treated more successfully by other means. For instance, the antibiotic metronidazole (Flagyl) is a drug many vets reach for to treat the loose stools all pets experience from time to time, often due to dietary indiscretion.

In this scenario, your pet isn’t dealing with a bacterial GI infection requiring aggressive drugs, rather, he or she ate something they shouldn’t have or you changed their diet too quickly.

Research shows even a short course of this “diarrhea medication” can decimate the microbiome, making future GI issues much more likely, not less. Even more frustrating, studies have also found that probiotics and other side effect-free treatment options can be equally as effective for diarrhea resulting from stress or dietary indiscretion.

In some cases, antibiotics are absolutely warranted because raging infection is present. But it’s important not to guess at what antibiotic is best to treat it. Guessing can result in delayed effective treatment, antibiotic resistance and microbiome disasters.

So how does your vet know what antibiotic will be the correct choice to effectively resolve the infection with the least amount of drug in the shortest time? By performing culture and sensitivity testing.

Building and Maintaining a Healthy Microbiome

If your pet has been given antibiotics, or must continue to take drugs that compromise the integrity of the gut, providing a gut reparative plan or an ongoing gut support plan is something your integrative or proactive vet will automatically do (potentially assessing the microbiome damage and performing microbiome transplants).

One of the best ways to ensure your pet has a healthy microbiome is by restricting the amount of refined carbs in the diet to less than 20% of calories, including biome-building fermented foods (such as fermented veggies, broths and kefir), regularly including prebiotic-rich foods (my favorites to mince and mix into pet food are culinary mushrooms, asparagus, green bananas, burdock root and jicama) and if necessary, a probiotic supplement that restores and rebuilds the microbiome.

Your dog or cat should receive the majority of his nutrients from a fresh, whole food meal plan that contains lots of dietary diversity. When we interviewed famed microbiologist Dr. Tim Spector for The Forever Dog book he said he couldn’t think of anything more damaging to a pet’s microbiome than feeding the same highly processed food day after day; it makes achieving optimal health impossible.

The science is clear that food diversity is critical for gut health, but so is avoiding the unwanted chemical tagalongs that are formed in ultraprocessed pet foods as a result of multiple high-heat processing steps (which is how all kibble/extruded and canned pet foods are made).

Damaging advanced glycation end products found in high amounts in pet foods disrupt the microbiome (and negatively impact organ systems and immune health).3 Research also shows that minimally processed foods create a more diverse microbiome in dogs (vs. those fed kibble).4

Switching to fresher food diets, rotating ingredients/brands, or at a minimum, replacing highly refined treats with fresh foods and adding real food toppers are all things that will improve your pet’s GI wellbeing, and in turn, his or her overall immune function.

Pet Services




Follow Us