Healing Your Pet From the Inside Out

As a functional medicine veterinarian, my focus has always been to identify the root cause of disease and help animals heal using common-sense, science-backed approaches. Medications have their place, but they should be used thoughtfully and sparingly when they truly support recovery. More often, real healing comes from addressing diet, environment, lifestyle, and the microbiome, the foundational pillars of health that are too often overlooked.

Thirty years of treating gut issues in small animals led me to develop a 5-step approach to help my clients lay the foundation for a healthy gut, or to restore it, for their beloved companions. I share it now with you.

Review. Rework. Repair. Rebuild. Restore.

These five steps form the foundation for restoring gut health in animals. Every stage matters, and together they create a clear roadmap to healing. My goal is to empower my clients (and you, reading this information) to gain enough knowledge to feel confident and make well-informed decisions. When we know more, we make better choices and have fewer regrets. Keep learning and asking questions, because becoming the primary advocate for your pet’s health is the best gift you could ever give them.

I will share the information, options, and strategies. You and your hands-on support team will decide what’s right. If you’re looking to add an integrative or functional medicine vet to your team but don’t know how to find one, check out the directory at www.civtedu.org (telehealth consults are also available).

Step One: Review

We’ll begin with Review, understanding what’s happening inside your pet’s body and why. What are the root causes of chronic symptoms? There is an epidemic of inflammatory conditions in pets nowadays. Most of the “-itis” disorders: gingivitis, otitis, dermatitis, are simply different faces of the same underlying problem, persistent inflammation. This is what veterinarians see in practice every single day. And while conventional drugs may manage the symptoms of inflammation and other pesky recurring problems, they don’t prevent the body from further decline, nor do they address the root causes of why the disease occurred in the first place. That’s our job to figure out. So let’s get to work.

Most people believe that digestive problems are only linked with obvious symptoms: a dog with diarrhea, a cat vomiting on the rug, or a pet with bad gas and bad breath. These signs certainly can suggest a problem in the gastrointestinal tract, but they are only the tip of the iceberg. Many pets with significant gut dysfunction never show classic digestive symptoms at all. Instead, they may itch year-round, battle chronic ear infections, develop arthritis earlier than expected, or even struggle with behavioral problems like anxiety or aggression.

In my almost 30 years of small animal clinical practice, I have seen dogs whose seizures dramatically improved once their gut microbiome was addressed, and cats with arthritis whose mobility returned after their intestinal lining got repaired. These cases illustrate what science now confirms: the gut is not an isolated organ. It is ground zero for systemic health, and dysfunction within it can ripple out to nearly every organ system.

Sometimes the root cause of gut problems is apparent, such as repeated antibiotic use without gut repair, or severe infections that profoundly affect gut health, like parvovirus or Giardia. Other times, it can be complex: gluten-sensitive enteropathy with genetic roots, irritable bowel syndrome that science has linked to early spay or neuter, or chronic dysbiosis driven by hidden food sensitivities and environmental stressors.

The good news is that this tangled web can be unraveled. By carefully reviewing root causes, reworking your pet’s diet, repairing the intestinal lining, rebuilding microbial diversity, and restoring balance, we can give our pets the strong foundation they need for lifelong vitality.

Let’s examine two closely related concepts: dysbiosis, or microbial imbalance, and leaky gut syndrome, also known as increased intestinal permeability.

Dysbiosis describes a microbial imbalance — too few beneficial bacteria and too many harmful or opportunistic ones. A healthy gut microbiome functions like a vibrant ecosystem: thousands of species coexist, competing for resources and keeping each other in check. Beneficial organisms ferment fibers into short-chain fatty acids (SCFAs), such as butyrate, which nourish the epithelial cells lining the gut. They help train the immune system to recognize friend from foe, and they even manufacture neurotransmitters like serotonin and gamma-aminobutyric acid (GABA)¹.

When dysbiosis develops, this harmony collapses. Opportunistic bacteria and yeast proliferate, producing toxic byproducts like lipopolysaccharides (LPS) that inflame the gut lining. Protective SCFA production declines, the mucus layer thins, and tight junctions between epithelial cells weaken².

Leaky gut refers to the breakdown of the intestinal barrier. Under normal conditions, the intestinal wall functions as a smart filter: digested nutrients are absorbed into circulation, while toxins, microbes, and undigested food particles are kept out. But when inflammation, drugs, or toxins damage this barrier, microscopic gaps form between epithelial cells. Large food fragments, bacterial toxins, and microbes slip into the bloodstream, where the immune system detects them as foreign invaders³,⁴.

The immune system responds by launching a defense: producing antibodies, releasing inflammatory cytokines, and staying in a state of constant hypervigilance. Over time, this low-grade, systemic inflammation sets the stage for chronic conditions such as skin allergies, behavioral changes, autoimmune disorders, and even neurological disease.⁵

Digestion 101

First let’s review how digestion works when it’s healthy. Food enters the mouth, where chewing is sometimes optional for dogs. In the stomach, hydrochloric acid and pepsin denature proteins and kill pathogens. The chyme (a slurry of partially digested food and gastric juices) then enters the small intestine. Here, bile salts from the gallbladder emulsify fats, and pancreatic enzymes cleave proteins and carbohydrates into absorbable units.

The small intestine is lined with villi and microvilli, creating a surface area the size of a tennis court in a medium-sized dog. These structures are coated with mucus and colonized by microbes. Beneficial bacteria ferment dietary fibers into SCFAs such as acetate, propionate, and butyrate. These metabolites fuel epithelial cells, strengthen tight junctions, and suppress inflammation.

When digestion is impaired, perhaps due to low stomach acid, inadequate enzymes, or microbial imbalance, undigested food fragments reach the colon. There, they ferment abnormally, producing gas, bloating, and toxins. This chronic irritation erodes the mucus layer and loosens tight junctions, setting the stage for leaky gut.⁶

Beyond Obvious Signs of Digestion Issues

Because the gut communicates with nearly every organ system, its dysfunction manifests in diverse ways. Aside from the obvious signs, non-digestive signs like those listed below are more deceptive:

• Allergies that worsen over time, as more partially digested food proteins cross the leaky barrier, abnormally stimulating the immune system
• Year-round itching, hot spots, and recurrent ear infections
• Behavioral changes such as anxiety, aggression, or hyperactivity
• Chronic bladder inflammation or sterile cystitis
• Joint pain, chronic inflammation and autoimmune conditions
• Seizures, thyroid imbalance, or even cancer (GI lymphoma) in advanced cases.

These examples highlight a critical truth: gut dysfunction often masquerades as other diseases. Unless the root is addressed, treatments only mask symptoms.

Why Pets Can Look “Healthy” and Still Be Inflamed

One of the most insidious aspects of dysbiosis and leaky gut is that pets may appear perfectly fine —shiny coat, healthy weight, playful energy — while chronic inflammation simmers unseen. This “silent inflammation” can last years before disease becomes obvious.

By the time a dog “suddenly” develops food or environmental allergies in middle age, the groundwork was laid long before. Each antibiotic, each steroid taper, chemical exposure, and bowl of kibble slowly chipped away at gut resilience.

Recognizing this hidden process empowers us to act preventively. Supporting gut health early in seemingly healthy pets reduces the risk of future disease. And for those already suffering, repairing the gut can dramatically shift outcomes, often transforming both quality and length of life.

Dysbiosis and leaky gut are not fringe theories; they are central to understanding chronic disease in pets. By defining them, examining how they develop, and mapping their clinical signs, we can finally grasp why so many seemingly unrelated conditions trace back to the gut.

The gut is truly “ground zero.

Common Root Causes of Gut Damage

Gut problems develop slowly, over time, as little injuries stack up until the intestinal lining and the microbes living there can no longer keep up.

The gut behaves like a strong, protective castle wall designed to keep invaders out, while letting in the good stuff. But antibiotics, ultra-processed kibble, environmental toxins and chemical exposures create micro-cracks in that wall. One crack may not cause much trouble, but after years of repeated hits, the wall begins to crumble. That’s when dysbiosis and leaky gut set the stage countless other chronic issues.

Let’s walk through the most common culprits, one by one.

Antibiotics: Both Lifesaving and Microbiome-Wrecking

Antibiotics are miracles when we need them and no one should feel guilty for using them when they’re truly necessary. They can save lives. But they don’t discriminate. Just like a wildfire burns through a forest without sparing the helpful plants, antibiotics wipe out beneficial microbes along with the bad ones.

Most animals treated with antibiotics appear fine after early use, but some go on to develop food allergies, itchy skin, or chronic ear infections months later.

Metronidazole (commonly known as Flagyl) is one of the most frequently prescribed drugs for dogs with diarrhea, but its widespread use comes at a cost. While it may temporarily reduce symptoms, research shows that metronidazole significantly alters the gut microbiome, reducing both the richness and diversity of beneficial bacterial populations⁷. These changes can persist long after treatment ends, leading to long-term disruption of microbial balance.

Here are my rules for antibiotic use:

• Use only when truly necessary (such as for bladder infections, dental infections, or other confirmed bacterial problems that are not responding to multimodal integrative support), not for minor issues that can be effectively managed without them (like a hotspot).
• Give the full course of antibiotics exactly as prescribed, don’t stop early, even if symptoms improve.
• Support the gut during and after antibiotic use with high-quality probiotics to help reseed beneficial bacteria.
• Include fermented foods (such as kefir, fermented veggies, or pet-safe yogurt) and prebiotic foods (fiber-rich veggies, mushrooms, or dandelion greens) to nourish the microbiome.
• Monitor your pet for side effects (like diarrhea, lethargy, or loss of appetite) and report concerns to your veterinarian.
• Keep a record of which antibiotics your pet has taken and how they responded, to guide future medical decisions.

Ideally, ask your veterinarian to run culture and sensitivity testing prior to administering antibiotics to ensure the one prescribed is the most effective choice.

Steroids, NSAIDs, and Acid Blockers: The Hidden Gut Costs

Next are the “everyday drugs”; medications many pets end up on at some point in their lives. Steroids like prednisone, NSAIDs (non-steroidal anti-inflammatory drugs) like carprofen, and acid blockers that are prescribed for vomiting or reflux.

Steroids can be lifesaving for severe allergic reactions, but they also thin the intestinal lining and suppress protective immune factors. NSAIDs interfere with prostaglandin production, reducing blood flow to the gut lining and weakening the protective mucus barrier. Over time, microscopic erosions and increased intestinal permeability can occur.

Acid blockers, while often helpful for short-term vomiting, reduce stomach acid so much that dietary proteins are not broken down properly. Large fragments end up in the intestines, where they may act as allergens. In people, proton pump inhibitors (PPIs) are well-documented to shift the microbiome toward dysbiosis, reducing beneficial taxa and increasing pathogenic ones and the same mechanisms apply to pets.

Ultra-Processed Pet Food: the Price we Pay for Convenience

Every scoop of ultra-processed pet food comes with a hidden cost—and it’s not just on your wallet. When we trade real, living nutrition for heat-extruded pellets and long shelf life, our pets pay the price with inflammation, metabolic stress, and chronic disease. Over time, these convenience diets quietly chip away at vitality, gut health, and immune resilience. What looks like “complete and balanced” on the label often means stripped, synthetic, and biologically foreign to the body. The good news? Once you understand the price of processed, you can start investing in real nourishment that gives life back—bite by bite.

The obesity-“pet food”-connection: How commercial pet foods are formulated is also a problem for most pets. AAFCO (the organization that sets nutrient requirements for pet food in the US) requires manufacturers to formulate for active pets, meaning there’s a higher number of calories per gram of food. More than 60% of pets are overweight, so if you feed the amount on the bag your animal will get the appropriate amount of required vitamins and minerals the body needs to maintain health, as well as an excessive number of calories. If you reduce the amount you feed (and feed less than the amount recommended by the company) your pet will be protein and/or nutrient deficient.

This is a horrible decision pet parents must make: maintain their pet’s ideal body weight (and likely be nutrient deficient) or feed the amount of food recommended and have their pet slowly gain weight. The only solution to this formulation problem is to feed pet foods or recipes that have been formulated on a metabolic basis, meaning the entire recipe is built around providing sufficient amounts of vitamins, minerals and protein with fewer calories.

Steve Brown has analyzed hundreds of commercial pet foods across all pet food categories. He has found that no commercial brands are currently implementing this required approach for accurate pet food formulation, and one of the many reasons our group of nutritionists and veterinarians has developed new formulation parameters called Optimal Nutrient Recommendations (ONR™). By formulating to meet the needs of all activity levels we can be assured our animals are well nourished, regardless if they are less active or highly active. This also eliminates the risks of diet-induced nutritional deficiencies (like nutritional Dilated Cardiomyopathy) or excesses (copper hepatopathy, or copper excesses).

Our goal is for every pet food manufacturer in the world to adopt this updated and accurate formulation method. Currently, the only recipes that have been formulated metabolically, to my knowledge, are those found in our recipe book, The Forever Dog Life.

High heat processing also negatively alters the structure of food, denaturing proteins, oxidizing fats, inactivating vital enzymes, decreasing vitamin and mineral content (enough that synthetics have to be added back in after processing), and it also causes one of the biggest hidden disease-causing culprits the pet food industry doesn’t want you to know about, AGEs.

How AGEs Stress the Body

Extrusion, the manufacturing method used to make most kibble, generates advanced glycation end products (AGEs) and advanced lipoxidation end products (ALEs), compounds formed when sugars and proteins or fats are exposed to extreme heat. Every cell of your pet’s body has a receptor for these heat-created toxins, alerting the cells that there’s noxious molecules circulating in their system.

AGEs/ALEs cause massive inflammation, creating more pro-inflammatory compounds, damaging gut barrier integrity, and accelerating oxidative stress⁵ ⁶. Thousands of research papers in both human and animal models link the consumption of AGEs to chronic diseases, metabolic dysfunction, and inflammatory gut disorders, raising serious concerns about their long-term effects in pets (and the last thing the pet food industry wants you to know about).

Additional concerns that come with feeding mostly engineered food particles:

• Low moisture content (around 10% in kibble versus 70–80% in fresh food) leads to chronic, low-grade dehydration that compromises the mucus barrier protecting the intestines^.
• Additives, preservatives, dyes challenge the microbiome and immune system daily.
• Monotonous diets narrow microbial diversity. Historically, animals consume a variety of different foods, and each one nourishes the microbiome in a variety of different ways. Eating the same food every day doesn’t achieve optimal gut diversity.
• Ingredient quality is a problem: Most pet foods are “feed grade,” meaning they’re made with terrible quality ingredients that failed human food inspection. Look for pet foods made with human-grade ingredients to help reduce exposures to common contaminants in pet foods including heavy metals, mycotoxins and pesticide residues.

In practice, I’ve seen countless cases where a simple switch from ultra-processed food to fresh, minimally processed meals resulted in dramatic turnarounds. Dogs and cats with chronic loose stools (or lifelong constipation) developed perfect bowel movements. Cats with itchy skin finally stopped over-grooming. Your pet’s gut was designed to thrive on real food; it’s our job to make it healthy enough to be able to assimilate and absorb the foods their bodies were meant to consume (and break the addiction to their current junk foods, it’s just as hard for pets as it is for us).

I recommend feeding the best food you can afford to feed; the less processed, the better. If you can only afford to feed kibble, then you can focus on adding as many fresh food toppers and real food treats as possible to help diversify your pet’s gut.

We wrote a New York Times best-selling recipe book, The Forever Dog LIFE, to give you direction and inspiration if you want to make raw, gently cooked, baked, or crock pot nutritionally complete recipes for your dog or cat, and don’t know where to start.

The Effects of Spay/Neuter on the Gut and Immune System

Most people don’t realize that early spay/neuter can also influence gut health. Hormones guide the development of mucosal immunity, and when they are removed too early, the gut’s immune defenses may not mature fully.

Secretory IgA — the antibody that protects mucosal surfaces — plays a vital role in neutralizing pathogens before they cross the intestinal barrier. Some dogs, particularly German Shepherds, already suffer from IgA deficiency, which predisposes them to chronic enteropathies. Early spay/neuter appears to compound this weakness, leaving some pets especially vulnerable.

Desexed dogs had a significantly greater risk of atopic dermatitis (allergic skin reactions), autoimmune hemolytic anemia, hypothyroidism, Addison’s disease, immune-mediated thrombocytopenia, immune-mediated polyarthritis, lupus, and inflammatory bowel disease than intact dogs⁹.

These dogs often benefit from targeted support, including colostrum, omega-3 fatty acids (DHA/EPA), IgA supplements¹⁰, as well as glandular support. Hormone replacement therapy is also something I have provided for my own rescue dog, and is being researched by the Parsemus Foundation (www.parsemus.org also has a directory of vets that provide hormone-sparing sterilizations). If you’re looking to see what your pup’s hormone status looks like, post-neuter, ask your vet to run a baseline endocrine panel from the University of Tennessee’s endocrinology lab. Cats have an entirely different reproductive system and do suffer from the long list of degenerative conditions now linked to lifelong hormone deficiencies in dogs.

Environmental Gut Stressors in the Home and Yard

Our modern environments subject pets to countless chemical exposures every day. Many of these compounds act as endocrine-disrupting chemicals (EDCs), interfering with the microbiome and damaging the gut lining.

• Glyphosate is the most widely used herbicide in the world. Research shows it can alter the gut microbiome, reduce beneficial commensals, and damage intestinal tight junctions ¹¹.
• Tap water pollutants such as chlorine, fluoride, heavy metals, pharmaceutical residues, and microplastics are frequently present in municipal supplies. Chlorination byproducts have been linked to microbiome disruption and endocrine interference.
• PFAS (“forever chemicals”) found in stain-resistant fabrics, non-stick cookware, and protective sprays persist in the body and are associated with thyroid dysfunction, reproductive harm, and immune suppression ¹².
• Household chemical off-gassing from air fresheners, cleaning products, and fabric protectants release volatile organic compounds (VOCs) such as phthalates and synthetic musks, many of which act as hormone disruptors.
• Microplastics and their additives, such as bisphenols and phthalates, leach endocrine-active substances. Microplastics also act as carriers for other pollutants, adding to the toxic burden.
• Flea and tick pesticides can be neuroactive and endocrine-interfering. Chronic exposure has been shown to affect the gut–brain axis and detox pathways in animals.
• Mold and mycotoxins from contaminated homes impair gut epithelial cells, drive inflammation, and suppress immune function.

Although each of these exposures may seem small, they are daily and cumulative. Over time, constant contact with these contaminants degrades gut barrier integrity, shifts microbial communities, and disrupts hormonal balance. Filtering water and air, avoiding PFAS-containing sprays and cookware, replacing synthetic cleaning and fragrance products, rotating safer pest-control strategies, and mitigating mold are simple but profound steps to protect both gut health and overall resilience.