Restore: The Final Step in Rebuilding Your Pet’s Gut Health

Your pet’s microbiome is the foundation of lifelong wellness. Learn how targeted probiotics, soil-based organisms, and gentle prebiotic foods can help restore balance, resilience, and vitality; one microbe at a time.

Our pets face challenges nowadays that their wild ancestors never did due to lifestyle and environmental stressors discussed in steps one through four on canine gut health: Review, Rework, Repair, Rebuild, Restore. This is where probiotics come in. Probiotics are not a luxury or an optional “add-on” for today’s dogs (and cats), they are foundational. By reseeding the gut with targeted, beneficial organisms, probiotics help restore what has been lost, strengthen intestinal barriers, and support whole-body resilience.

Probiotics are not just “digestive aids.” They are living organisms that dynamically interact with the gut, the immune system, and even the nervous system. Each strain has unique properties, almost like a unique “job description.” Some strengthen the gut lining, others fight pathogens, while others communicate directly with the brain. And here is a critical distinction: not all probiotics are interchangeable.

Sensitive Pets: Starting in the Right Place

For pets with very fragile or sensitive digestive tracts that react to almost every new food or supplement, the way we approach gut healing matters. These animals often cannot tolerate large microbial loads from fermented foods, or even any new foods without major problems. The histamine and acids naturally present in ferments, while health-promoting for many, can inflame an already irritated intestinal lining. Concentrated prebiotic supplements can cause similar problems. They feed bacteria indiscriminately, and in conditions like small intestinal bacterial overgrowth (SIBO), that fuel can worsen gas, bloating, and abdominal pain.

For these delicate pets, probiotic supplements are the safest and most effective first step. They provide specific organisms at measured doses. We can start with very small amounts, carefully observing tolerance, and increasing gradually. Low and slow wins the race when it comes to beginning protocols for super sensitive animals. This controlled, predictable approach gently nudges the gut toward balance without overwhelming an already stressed system. Once stability is achieved, other microbial foods can be layered in.

Soil-Based Organisms (SBOs): Environmental Allies for Gut Resilience

Soil-based organisms (SBOs) are spore-forming probiotics that originate in the earth, nature’s original probiotic reservoir, and bring vital ecological benefits to the gut. As dogs have become increasingly disconnected from natural environments, their exposure to these environmental microbes has drastically diminished.

SBOs are exceptionally hearty, capable of surviving extreme conditions, including the acidity of the stomach. Once inside the gut, they play a vital role in restoring microbial diversity, supporting immune resilience, and resisting pathogenic overgrowth.

Core Benefits of SBOs include pathogen control: they naturally produce antimicrobial compounds that inhibit harmful bacteria, including Clostridium and E. coli. Immunomodulation: SBOs help balance the immune system, reducing inappropriate inflammatory responses and supporting mucosal immunity. They enhance microbial diversity by reintroducing diversity and competitive exclusion, which is especially important after exposure to antibiotics or heat-processed diets. They maintain gut integrity, supporting epithelial tight junctions and reinforcing the gut barrier against leaky gut and inflammatory damage.

SBOs act as environmental "educators," reintroducing important microbial interactions that today’s dogs, often deprived of natural soil exposure, no longer receive.

The two most celebrated soil strains that build resilience and microbiome diversity are Bacillus subtilis¹ and Bacillus clausii². B. subtilis is known for its ability to support gut mucosal immunity by stimulating beneficial immune signaling and promote microbiome balance in animals under stress, including post-drug use that disrupts gut balance (heartworm meds, flea/tick meds, etc). B. clausii is most famous for modulating immune responses, especially in dogs with allergy-like or inflammatory tendencies, enhancing epithelial resilience and tight junction function for better gut integrity, promoting resistance to colonization by opportunistic pathogens like Clostridium and Escherichia coli.

SBOs After Antibiotic Therapy

When a course of antibiotics ends, the gut ecosystem is often unstable. Beneficial microbes have been depleted, leaving gaps in the community that opportunistic organisms are quick to exploit. SBOs are ideally suited for this recovery phase. Because they are robust colonizers, they rapidly occupy these vacant niches. They produce metabolites such as antimicrobial peptides and short-chain fatty acids that suppress pathogens while nourishing beneficial bacteria). They also reduce oxidative stress and stimulate epithelial repair, helping the intestinal barrier rebuild itself after antibiotic injury.

For these reasons, SBOs are one of the few probiotics that can be given both during and after antibiotic therapy with great benefit. They do not just survive the treatment; they help stabilize and restore the ecosystem in its aftermath.

Keeping Restored Microbiomes Resilient and Healthy

Choosing species-specific probiotic strains, when administered in adequate amounts, confer unique health benefits. They help maintain microbial diversity, compete with pathogens for nutrients and attachment sites, and produce metabolites such as short-chain fatty acids that nourish the gut lining.

Using canid-derived probiotics can offer tremendous benefits over human strains. Most pet probiotics on the market are borrowed from human probiotic manufacturers, and aren’t adapted to the metabolic, immune, or thermal environment of dogs or cats. They’re not designed to survive the journey through a carnivore’s GI tract, and many lack evidence of efficacy in the species they’re sold for. Emerging research now confirms that species-specific probiotics, isolated from healthy members of the same species, offer more targeted benefits. These strains are naturally adapted to the host animal’s microbiome, pH, bile levels, temperature, and immune landscape.

Avoid “All-in-One” Gut Health Products

Many pet parents come to me after trying every “gut health” supplement they can find and most of these formulas contain a little bit of everything. While that might sound comprehensive, these blends can complicate rather than clarify the healing process.

Combination products that mix probiotics, prebiotics, enzymes, nutraceuticals, herbs, vitamins, and minerals may contain some helpful ingredients, but also others that aren’t appropriate for your pet’s current condition. When reactions occur, it becomes nearly impossible to identify which ingredient caused the problem.

One common example is products that combine probiotics and prebiotics. While both can be valuable tools, they serve different purposes and should be used strategically, not simultaneously by default. Most commercial probiotic formulas include added prebiotics, often labeled as inulin, FOS (fructooligosaccharides), or chicory root. These compounds are fermentable fibers that feed gut bacteria, which can be beneficial in some cases, but problematic in others.

For example, in pets with the incredibly common problem of small intestinal bacterial overgrowth (SIBO) or dysbiosis affecting the upper GI tract (most cases I see), prebiotic supplements can worsen symptoms by fueling excessive bacterial fermentation. This leads to increased bloating, gas, and discomfort. For this reason, I don’t recommend prebiotic supplementation unless diagnostic testing confirms that it’s needed.

Whole-Food Sources of Prebiotic Fiber

For most pets, a safe, simple, and affordable approach to nourish the beneficial bacteria already present in your pet’s gut is to provide fresh, whole prebiotic-rich foods. These foods naturally contain the fermentable fibers that “good bugs” thrive on, without the concentrated doses or side effects that sometimes come with commercial prebiotic powders.

Here are some prebiotic-rich foods you can chop into small, bite-sized microbiome building pieces:

• Green bananas (slightly underripe): A gentle source of resistant starch that supports butyrate-producing microbes³.
• Cooked and cooled sweet potatoes: When cooled, these form resistant starch that fuels beneficial bacteria. Smear on a lick mat or stuff an interactive toy!
• Asparagus tips: Contain inulin and other fibers that promote Bifidobacteria growth.
• Jerusalem artichokes (sunchokes): Very rich in inulin, start with tiny amounts to avoid gas.
• Chicory root (fresh or lightly cooked): One of the highest natural sources of inulin.
• Dandelion greens: Provide prebiotic fibers along with liver-supporting phytonutrients.
• Buried greens (turnip, beet, or mustard greens): Contain complex carbohydrates that encourage microbial diversity. Steam and cool before feeding.
• Apples (with peel, finely chopped): Contain pectin, a gentle fermentable fiber for colonic health.
• Blueberries: Supply polyphenols that modulate the microbiome and support beneficial species.
• Pumpkin (cooked): Offers soluble fiber that helps normalize stool consistency and support gut flora.
• Carrots (lightly cooked or grated): Rich in soluble fiber and phytonutrients beneficial for gut motility.

Start slowly, just a tiny bite a day, and rotate different foods throughout the week. Variety, rather than volume of prebiotic fibers, is what helps build a resilient, balanced microbiome over time.

It’s important to remember that rebuilding the gut microbiome doesn’t require perfection, it requires consistency. Over time, with the right foods and targeted support, beneficial microbes gradually recolonize and restore balance. Simpler is often better, especially when you’re working with a sensitive gut.

New Frontiers in Probiotic Research

Psychobiotics: Calming the Gut–Brain Axis

The newest frontier in probiotic research involves psychobiotics — strains that influence mental and emotional health through the gut–brain axis. Certain strains, such as Lactobacillus plantarum LP815, produce gamma-aminobutyric acid (GABA), a naturally produced neurotransmitter that calms the nervous system⁴. By lowering cortisol and supporting vagal nerve signaling, these strains help reduce stress-induced diarrhea, anxiety-related GI symptoms, and even chronic bladder inflammation in cats. While still an emerging field, the potential of psychobiotics is profound — offering a way to soothe both the gut and the mind simultaneously.

• Reduce stress. By influencing the vagus nerve and the hypothalamic–pituitary–adrenal axis, GABA-producing strains help lower cortisol.
• Improve resilience. Pets under chronic stress (such as rescues, anxious dogs, or cats prone to cystitis) may benefit greatly from these probiotics.
• Support the gut lining. Stress reduction indirectly strengthens the gut barrier, since cortisol otherwise erodes tight junctions.

According to exciting new research, these strains hold promise for anxious pets or those with stress-related gut issues, not to mention pets with mood disorders, or miserably itchy animals with aggravated mental states. In one study, after just 4 weeks on a GABA producing probiotics dogs had reduced fear and noise-based aggression, more restful and consistent sleep, improved mood and reduced reactivity, better energy and emotional balance, and faster settling after owner departure⁵.

Bacteriophages: Targeting E. Coli Overgrowth in the Gut

Bacteriophages, often called phages, are naturally occurring viruses that specifically infect and destroy bacteria without harming human or animal cells. They work by attaching to a bacterial cell, injecting their genetic material, and hijacking the cell’s machinery to replicate themselves—ultimately causing the bacteria to burst and die. This highly targeted approach makes them powerful allies in balancing the gut microbiome. Deerland’s PreforPro is a unique fiber-free prebiotic that harnesses the precision of phages to target problematic bacteria such as E. coli, helping reduce overgrowth while leaving beneficial microbes intact. By selectively reducing excessive E. coli proliferation, PreforPro supports a healthier, more resilient gut environment if microbiome testing reveals an overgrowth of E. coli.

When to Seek Advanced Care

Some pets require deeper investigation. If your animal continues to struggle despite careful diet, supplements, and environmental changes, or if conditions such as severe IBD, chronic pancreatitis, or unexplained weight loss persist, it may be time for advanced diagnostics. Tests like ultrasound and endoscopy can uncover hidden causes that even the most advanced blood panels miss.

If your pet is declining, seek care now. If your animal fails to improve after multiple interventions, ask your veterinarian for a referral to an internal medicine specialist. Acting sooner gives your pet the best chance at recovery through tailored treatment.