Some supplements provide such foundational support that they benefit nearly every case of dysbiosis no matter what the underlying cause is. These “universal helpers” assist the body’s natural processes, reducing the workload of an already stressed gut. When combined with a comprehensive microbiome restoration program, they help create the internal environment needed for full repair and lasting resilience.
Because every gut story is unique, there’s no one-size-fits-all formula. Still, most veterinarians agree on this universal framework for rebuilding gut health, and most integrative and functional medicine practitioners recognize a handful of core supplements that consistently deliver exceptional results when restoring microbiome balance.
Foundational Supplements to Consider
Digestive Enzymes
Digestive enzymes break down macronutrients into their usable components: proteases split proteins into amino acids, lipases cleave fats, and amylases convert starches into simple sugars. This ensures complete digestion before food reaches the colon, reducing the substrate available for harmful bacterial fermentation1.
A high-quality enzyme blend should target proteins, fats, carbohydrates, and plant fibers while providing cofactors that enhance digestive efficiency. Look for formulas containing proteases (such as fungal protease, bromelain, and papain), lipase for fats, and amylase for starches. Additional enzymes, cellulase, hemicellulase, xylanase, beta-glucanase, and lactase, help break down plant fibers and sugars that often cause bloating or gas.
Some blends also include microbial pancreatin (to mimic pancreatic secretions), along with ox bile and taurine to support fat breakdown and absorption. Together, these ingredients create a more complete digestive profile that mirrors the capacity of a healthy gut. The only time digestive enzymes should be avoided is when an animal has active erosions or ulcers in the GI tract.
Stomach Acid and Bile Support
Adequate stomach acid and bile salts are essential for proper digestion, especially important for animals that have been on acid-blockers or antacids. Pets with inadequate levels of stomach acid often experience belching or burping. Gastric juices help break down proteins and kill pathogens, while bile emulsifies fats for absorption. When stomach acid or bile are insufficient, large, undigested food particles reach the lower intestines, overloading the microbiome and immune system2.
Functional medicine veterinarians sometimes use betaine HCL and pepsin to restore healthy stomach pH—though never in animals with ulcers. Ox bile (often paired with taurine and choline) can be helpful for pets with sluggish gallbladders or gastroesophageal reflux (GERD), improving the emulsification and absorption of dietary fats.
Colostrum
Colostrum contains immunoglobulins, lactoferrin, and growth factors that protect and repair mucosal tissues while supporting secretory IgA levels3—an essential part of the gut’s immune defense. Beneficial for spayed and neutered animals, those suffering from chronic or antibiotic resistant infections4.
When Testing Shows Imbalances, These Two Protocols Are Go-To Choices
When a microbiome analysis shows an imbalanced microbiome or a GI blood test shows nutritional deficiencies that compromise mucosal repair, two evidence-based interventions can help restore equilibrium: fecal microbiota transplantation (FMT) and micronutrient repletion. These protocols complement each other by rebuilding microbial diversity while supplying the nutrients required for epithelial renewal and immune balance.
Fecal Microbiota Transplantation (FMT)
FMT, sometimes called “poo pills,” transfers beneficial microbes from a healthy donor into the gut of an animal with dysbiosis. Unlike probiotics, which typically contain a handful of strains, FMTs provide a full microbial ecosystem that more closely resembles the diversity of a natural gut. This reseeding process is a science-backed way to help restore microbial balance, suppress harmful overgrowths, and improve digestion, immunity, and resilience5. FMT can be administered as enteric-coated oral capsules or rectal infusions—both designed to deliver living microbes directly where they’re needed.
- FMT isn’t a magic bullet: one large retrospective study of 41 dogs with chronic enteropathy found that 31 of 41 responded (statistically significant reduction in clinical index) but response correlated with the baseline dysbiosis severity: dogs with more severe dysbiosis responded less well6.
- Emerging research shows behavioral links: a 2025 study found that gut microbiota composition in pet dogs could predict anxiety or aggression groupings; the genus Blautia was strongly implicated in anxiety7.
- A 2025 study on microbial diversity in dogs emphasizes that dysbiosis is linked not only to GI disease but metabolic disorders and behavioral issues8.
When FMTs Are Most Useful
FMT is particularly beneficial for chronic or severe dysbiosis, especially when conventional therapies fail:
- Chronic enteropathy or IBD: Dogs with persistent diarrhea or inflammatory bowel disease that do not respond to diet changes or medication often stabilize after FMT.
- Antibiotic-resistant infections: In human medicine, FMT is a proven therapy for recurrent Clostridium difficile infections, and emerging veterinary research suggests similar potential for pets facing resistant gut pathogens.
- Severe microbiome depletion: Repeated antibiotic use, chemotherapy, or prolonged illness can strip the microbiome of diversity. FMT helps reseed the gut with a balanced community.
Legacy Biome Healthy Gut Restore FMT is a capsule-based transplant sourced from rigorously screened donor dogs raised in low-chemical environments. It’s formulated to rebuild gut ecology and support immune balance while reducing antibiotic reliance.
AnimalBiome DoggyBiome Gut Restore Supplement offers a similar capsule-based approach, delivering thousands of dog-specific microbes to help rebalance chronic digestive and skin issues more comprehensively than traditional probiotics.
Micronutrient Repletion
Chronic gastrointestinal disease often leads to nutrient deficiencies due to malabsorption, maldigestion, or microbial imbalance. The most common deficiencies include cobalamin (B12) and folate (B9), but vitamin D and omega-3 fatty acid deficiencies are also frequent. Except for omega 3’s, always test before supplementing, as unnecessary excess can create its own imbalances.
Correcting micronutrient deficiencies enhances the effectiveness of microbiome therapies like FMT, as epithelial repair, mucus production, and immune signaling all depend on adequate nutrient status. Vitamin D, in particular, influences antimicrobial peptide production and barrier integrity, while B12 and folate are essential for mucosal cell turnover. Omega-3 fatty acids further regulate inflammation, aiding tissue regeneration and microbial symbiosis.
Omega-3 Fatty Acids
Omega-3 fatty acids help regulate inflammation and promote resolution, shifting immune responses away from gut-damaging cytokines9. Once stools are formed and stable, begin supplementation with EPA and DHA at 50 mg/kg/day, gradually increasing to 100 mg/kg/day as tolerance improves. For fish-sensitive pets, algal oil is an excellent plant-based option.
Combining omega-3s with digestive enzymes can enhance their absorption. Phospholipid-rich sources such as squid, herring roe, and krill oil tend to be better tolerated than refined ethyl ester forms of fish oil. This is the only nutrient I recommend giving without first testing to see if pets are low. I’ve done so many tests on pets with sick guts that I quit recommending testing before treating because they were all universally deficient. Now I recommend testing after 3 months of supplementation.
Supporting the body with the digestive tools it needs allows food to break down more efficiently, easing irritation and helping restore balance. While countless supplements and therapeutic approaches exist that veterinarians may use to aid recovery from chronic disease, the options shared here are meant to spark curiosity and guide you toward further exploration. Most importantly, remember this: there is every reason to be hopeful. With the right changes, your pet’s body has a remarkable ability to heal.
Why This Matters: The Big Picture on Gut Health for Dogs
Understanding that the gut microbiome is central to the overall health and wellbeing of your beloved companion is crucial. By intervening early and comprehensively, we set the stage not only for improved GI health, but for better systemic outcomes: less chronic inflammation, stronger immune resilience, balanced behavior, healthier skin and coat, and longer quality lives. The gut truly is the mirror and gateway to the rest of the body.
