Dysbiosis In Dogs
Dysbiosis is a term used to describe an imbalance in the population of microorganisms living in dogs' gut. The gut microbiome comprises a complex ecosystem of bacteria, viruses, fungi, and other microorganisms that play an essential role in maintaining the health and well-being of the host. These microorganisms help to break down food, produce vitamins, and protect against harmful pathogens.
In a healthy dog, the gut microbiome is in a state of balance, with beneficial bacteria outnumbering harmful bacteria. However, when this balance is disrupted, the population of harmful bacteria can increase, leading to a condition known as dysbiosis.
You may hear Dysbiosis termed Leaky Gut. They are related, but not quite the same.
In the photo: Dabo had dysbiosis as a very young puppy. A year or so later another puppy from the same breeder came to me with the very same issues. Dysbiosis can be inherited and a function of nutrition & diet.
I’ve seen dogs without solid poops for their whole lives — years!
What Is Dysbiosis in Dogs?
Dysbiosis is an imbalance in your dog’s gut microbiome — the delicate ecosystem of beneficial bacteria that influences digestion, immune health, inflammation, and even behavior. When that balance is disrupted — usually by stressors over time — your dog’s gut can become a breeding ground for harmful bacteria, yeast, or parasites, and lose its ability to do its job effectively.
And this goes far beyond the occasional upset tummy. An unbalanced microbiome puts your dog at risk for chronic inflammation, immune dysfunction, and eventually organ stress if left unsupported.
Common Causes of Dysbiosis
Many of today’s dogs are born with or develop dysbiosis due to a variety of compounding factors:
Processed or carbohydrate-heavy diets (like kibble)
Frequent or early-life antibiotic use
Toxin exposure (lawn chemicals, cleaners, flea meds)
Nutrient deficiencies (especially zinc, manganese, selenium, amino acids)
Chronic stress or anxiety
Poor dental or hygiene practices
Passed from an unhealthy mom (dysbiosis can start at birth)
Symptoms of Dysbiosis in Dogs
Some signs show up right in the gut — but many don’t. Watch for:
Diarrhea, gas, or soft stools
Weight loss or poor muscle tone
Dull coat or excessive shedding
Ear infections or itchy paws
Seasonal or year-round allergies
Anxiety, pacing, or sudden reactivity
Nutrient malabsorption despite good food
Recurring yeast or urinary infections
These are often signs the gut barrier is inflamed or compromised — which can set the stage for bigger issues like leaky gut, chronic inflammation, or immune system dysfunction down the road.
Trouble Switching Foods? That Might Be a Clue…
One of the first red flags of dysbiosis is the inability to transition to new foods without a reaction — even when those foods are healthy.
If your dog gets diarrhea every time you try to introduce raw, cooked, or new proteins — but seems “fine” as soon as you go back to the same kibble they’ve always eaten — this is a key indicator that something deeper is going on.
It’s not that the kibble is better — it’s that the gut is inflamed, and the body is relying on a learned survival response. Think of it as a false sense of stability. That old kibble may be easier for the body to predict and respond to (even if it’s harmful long term) — while real food requires a functioning gut to properly digest and absorb.
A similar pattern happens when adding a probiotic leads to worse symptoms, like bloating, gurgling, or loose stool. That often signals:
The gut lining is too inflamed to tolerate new bacterial activity
There’s overgrowth of pathogenic microbes competing for space
There are missing digestive enzymes or insufficient bile production
The immune system is hypersensitive to shifts in gut flora
This is why one-size-fits-all probiotic products often backfire — and why food-based gut healing must come first.
Why a “Stable” Gut Might Still Be Unhealed
Just because your dog isn’t having diarrhea doesn’t mean their gut is healthy.
Many dogs with dysbiosis don’t have outward digestive symptoms — until something tips the scale. The microbiome is resilient, but also compensates for damage over time. A dog who looks “fine” today could be:
Struggling with nutrient absorption
Living with low-grade inflammation
Accumulating toxins that aren’t being filtered
Compensating with secondary symptoms like skin issues or anxiety
If the gut barrier is compromised (often called “leaky gut”), it allows partially digested food proteins, toxins, and bacteria to enter the bloodstream. This sets off an immune cascade that can eventually lead to allergies, autoimmunity, or organ dysfunction — long after the initial gut issue appeared to calm down.
Long-Term Risks of Unresolved Dysbiosis in Dogs
Leaky gut — leads to food sensitivities, inflammation, and immune overreaction
Chronic inflammation — impacts joints, organs, and aging
Immune system dysfunction — contributes to allergies, infections, or autoimmunity
Nutrient deficiencies — even with high-quality food, absorption is impaired
Yeast overgrowth — itchy skin, stinky ears/paws, recurring infections
Behavioral issues — anxiety, reactivity, or cognitive changes from gut-brain disruption
Increased disease risk — including IBD, liver disease, and even cancer
Why I Start with a Liver Detox Before Transitioning Food
If your dog has signs of dysbiosis, sensitivities, or has trouble tolerating new foods, one of the most overlooked — but critical — first steps is to start with a gentle liver detox or cleanse diet.
Here’s why:
The liver is your dog’s master filter.
It processes waste, metabolizes medications, filters out toxins, and regulates inflammatory compounds. If the liver is congested or overwhelmed (which is often the case in dogs with gut imbalance), it simply can’t keep up — and new foods or supplements just become more stress on the system.A stressed liver impacts digestion.
The liver and gallbladder play essential roles in bile production — and bile is critical for breaking down fats, absorbing fat-soluble vitamins, and keeping the gut microbiome in balance. Without enough bile, your dog may experience loose stool, gurgling belly, or poor appetite when transitioning to healthier, richer foods.Detoxification frees up immune and digestive resources.
By gently supporting the liver and lymphatic system, we give the body a chance to clear out metabolic waste, balance inflammation, and calm the immune system. This makes it easier to handle food changes without triggering a flare-up of symptoms.It primes the gut to receive nourishment.
A clean-up phase helps reduce microbial overgrowth and mucosal irritation, creating a better environment for the gut to heal and repopulate with good bacteria. It’s like prepping the soil before planting new seeds.
Feeding a Dog with Dysbiosis
Food is your most powerful tool. And it needs to be digestible, nourishing, and anti-inflammatory. Start with:
Moist, whole food meals (raw or gently cooked)
Anti-inflammatory proteins and fats — variety matters!
Organ meats for key gut-healing nutrients like glutamine and B vitamins
Bone broth, collagen, and fermented foods (like fermented goat milk or Gussy Gut)
Avoiding kibble, synthetic vitamins, and starch-heavy treats
A fresh food transition may need to be slow and strategic — and that’s OK. A temporary reset with simple broths, enzyme-rich foods, or gut-friendly herbs may be necessary before jumping into a full fresh food bowl.
Supporting the Gut with Natural Supplements
Supplements can help repair, regulate, and repopulate the gut — but they work best when built on a solid nutrition foundation. A few gentle places to start:
S. boulardii — A beneficial yeast that helps regulate harmful pathogens, supports stool quality, and can be used safely even during antibiotics.
See AnimalBiome or 4 Leaf Rover
Gussy Gut (Fermented Vegetable Powder) — Delivers live beneficial bacteria, enzymes, and antioxidants without feeding raw plant matter.
See Gussy’s Gut
Spore-based probiotics — Typically more stable and less reactive for sensitive dogs than traditional dairy-based blends.
Colostrum and L-glutamine — Nourish the gut lining and immune cells.
Prebiotic-rich foods — like functional mushrooms
See MyCo Dogs or Real Mushrooms
All specifics about dosing and protocols are available in our client forum.
Herbs for Gut Health Support
Herbs can be incredibly helpful — soothing inflammation, calming spasms, and supporting the mucosal barrier. A few to consider:
Slippery Elm — Forms a soothing gel that coats and protects the digestive lining.
Marshmallow Root — Another demulcent herb that soothes irritated tissue.
Chamomile — Calms the gut and the nervous system — great for anxious dogs with gut issues.
Licorice Root (in DGL form) — Anti-inflammatory and protective for the stomach lining.
Oregon Grape Root or Goldenseal — Can be used short-term to support microbial balance.
Herbs are best chosen based on your dog’s symptoms, constitution, and TCVM energetics — not just their label. Reach out if you need help selecting the right blend
Visit Mtn. Rose Herbs for quality options. You may find quality products on Amazon but watch out for counterfeiters.
Essential Oils and Gut Healing
Essential oils can be part of your toolkit, especially when the digestive tract needs calming, or emotional stress is part of the picture.
Digestive blends that include: fennel, ginger, and peppermint can be applied to the abdomen for comfort.
Frankincense supports immune modulation and cellular healing.
For systemic support, the Raindrop Technique is an ideal way to activate detox, lymphatic drainage, and microbial defense while supporting emotional balance.
These oils must be used safely and appropriately — if you’re unsure, I’m here to guide you.
Top 5 Things You Can Do Today
Start rotating in small amounts of gently cooked or raw food (instead of kibble).
Try Gussy Gut or fermented goat milk for food-based probiotics.
Use S. boulardii during/after antibiotic use or digestive upset.
Support with herbs like slippery elm, marshmallow root, or chamomile. Ask me about Herbsmith Rx products.
Watch for signs of “false stability” — even calm guts may still need support.
Wrapping Up
Dysbiosis is more than just a stomach problem — it’s a warning sign from the gut-immune-brain connection. Whether your dog is showing obvious symptoms or not, the health of their gut affects everything from nutrient status to mood, inflammation, and long-term resilience.
The good news? Dogs respond beautifully to the right support — when we go slow, stay intentional, and work with the body instead of against it.
Want to go deeper with support for your dog through all life stages?
Join the client forum for ongoing support and resources!
Member Forum: https://members.welloiledk9.com
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Statements in this blog have not been evaluated by the FDA. Educational content only. Not intended to diagnose, treat, cure, or prevent any disease. Please do your own additional research, consult your vet as needed.
Call me to discuss using essential oils & herbs or customizing a diet for your dog.