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Written by: Sarah Seward-Langdon
Published on: 09/26/2025
If you often catch yourself talking about how your dog's poo looks on any given day, you already know gut health in dogs matters. But you might be surprised at just how much your pup’s digestive system does—it helps run their immune system, affects skin and coat quality, influences weight and nutrient absorption, and may even play a role in mood and behaviour.
In fact, up to 80% of a pet’s immune system is associated with the gut, which is why keeping those “good bugs” happy is such a big deal [1].
Here’s the tricky part: many different issues can look similar on the surface. A little diarrhea after sneaking garbage? That’s different from chronic diarrhea related to a lingering imbalance, parasites, or a food intolerance.
Gastrointestinal problems are among the most common reasons for vet visits, so knowing what’s “normal,” what’s a temporary blip, and what’s a red flag helps you get the proper support fast [2].
In this guide, we’ll break down the signs of poor gut health in dogs, some of the most common causes, when to see a vet, and natural ways to restore balance. Let’s ensure you can feel confident helping your best friend feel better from the inside out.
Your dog’s gut microbiome is a living ecosystem living inside the stomach, small intestine, and large intestine. It’s a bustling community of microorganisms (bacteria, fungi, viruses).
When that community is diverse and balanced, your dog is better equipped to digest food, absorb nutrients, produce vitamins, and remain resilient against illness. When it’s out of balance—sometimes referred to as dysbiosis—dogs can experience gastrointestinal troubles, skin issues, sluggishness, and more [1].
(Each sign below can have multiple causes. If you’re unsure or symptoms persist, check in with your vet.)
Does this sound like your dog? Frequent or alternating diarrhea/constipation, “on-and-off” loose stools, mucus or blood, or even recurrent vomiting. All of these can point to a gut imbalance [2].
If your dog’s stool is inconsistent or overly smelly, it can be a valuable clue. Likewise, chronically loose, very hard, excessively foul, or suddenly different stools are worth paying attention to.
If your dog toots occasionally, there’s no cause for concern—after all, some farting is normal. However, excess gas, distension, or discomfort can signal fermentation changes resulting from an imbalanced microbiome, abrupt dietary changes, or food indiscretion [2].
While we all love our dogs, we can agree that some of them have very strong-smelling breath. Beyond dental issues, your dog’s foul breath could indicate digestive imbalances or food intolerances that affect the upper GI tract and microbial populations [3].
The gut–skin axis is real. Dogs with skin allergies often show less diverse gut microbiomes. Itchiness, recurrent ear issues, dull/dry coat, or flakiness can be downstream effects of poor gut health and malabsorption [3].
If you notice your dog losing or gaining weight for no apparent reason, like no changes in their food or exercise, it could mean their gut isn’t absorbing nutrients properly or that an imbalance is affecting their metabolism [3].
Don’t wait it out—check in with your vet so you can get to the bottom of it quickly.
Hunched posture (“praying position”), painful belly, reluctance to move, or difficulty getting comfortable may reflect gastrointestinal pain. If your dog shows any of these symptoms, you should take it seriously and see a professional [2].
The gut–brain axis means that gut discomfort may manifest as lethargy, low mood, restlessness, or even anxiety. Subtle increases in thirst or a feeling that “just seems off” can accompany gut issues. Don’t ignore these symptoms if they persist or last for an extended period [1].
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✅ Non-GMO
✅ Ideal balance of Omega-3 compared to other products, like soybean oil.
✅ Canadian produced and operated.
Now that you know what symptoms to watch out for, here are some things that could cause an upset or unbalanced gut in your dog:
Dietary Indiscretion—ie. Trash, table scraps, “found food”—often triggers rapid-onset vomiting/diarrhea. The severity depends on what your dog eats [2]. Don’t panic if it was simply cooked broccoli, but be more worried if it was a piece of chocolate.
You’ll find that many dogs do not like abrupt diet changes. The microbiome adapts to what it’s fed. Fast switches, especially from kibble to raw, can cause gas, bloat, and loose stools [2].
Medications like antibiotics or NSAIDS may also be a cause:
Antibiotics reduce microbial diversity and can cause diarrhea that persists beyond the course of treatment [4].
NSAIDs and acid-lowering meds can alter the microbiome and irritate your dog’s GI tract [2].
Psychological or physical stress alters gut motility and microbial balance, leading to increased inflammation and diarrhea [2].
If your dog has food intolerances or allergies, this can present as vomiting, diarrhea, gas, or reflux. In these cases, a single-protein trial may help you to identify triggers [2].
Parasites and infections can also disrupt digestion and compete with beneficial microbes [3].
If your dog’s symptoms persist for more than 48 hours, consult your veterinarian.
When is it an emergency? If your dog appears to be very unwell, exhibits symptoms of bloat, has blood in their stool, experiences severe abdominal pain, is listless, or is dehydrated, or if you have a puppy/senior dog.
You should also be quicker to visit a vet if you have a dog with chronic conditions [2].
Remember to discuss any new diet or supplement plan with your veterinarian—especially if your dog has other health conditions.
High-quality, protein-forward, minimally processed foods support a healthier microbiome. Whole, dog-safe vegetables (e.g., leafy greens, carrots, green beans, broccoli) add natural fibre and antioxidants that feed beneficial bacteria [4].
Some evidence suggests raw or fresh diets can increase microbial diversity compared to high-carb kibbles—transition slowly if you choose to try this [2].
That being said, it doesn’t always need to be as complicated as switching your dog’s entire diet. Consider just adding some whole food ingredients to their bowls!
You could also add fibres like inulin, FOS, MOS. These selectively feed beneficial microbes and increase short-chain fatty acids (SCFAs), which help gut and immune health. Start low and go slow to avoid gas [4].
Probiotics can provide short-term relief and help rebalance the microbiome, especially during/after medication use or dietary changes.
Saccharomyces boulardii, a probiotic yeast, has been shown to be safe and beneficial for dogs, especially after antibiotic treatments [4]. Using probiotics in general is also helpful for maintaining your dog’s gut health and supporting the immune system [2].
Processing and heat can deplete natural enzymes in foods. Supplemental enzymes may help reduce belching, reflux, bloating, and irregular stools by improving the breakdown of macronutrients [2].
Mix new food with the old over several days to weeks, depending on sensitivity, so the microbiome has time to adapt [2]. This is especially helpful if your dog has a history of having a sensitive stomach.
Adequate water supports healthy motility, while appropriate fibre helps stool quality and feeds beneficial bacteria [1]. Make sure your dog has healthy access to both!
If you're worried about your dog’s gut, there are a few things you can do easily at home to help.
Do your best to keep routines predictable, add enrichment activities (such as sniff walks and puzzle feeders), and create calm spaces. Stress reduction helps normalize gut motility and microbial balance [2].
Spending safe outdoor time with your dog will help increase their exposure to diverse, harmless microbes found in soil and plants. This can support microbial diversity and help your dog’s overall gut microbiome [4].
Keeping up with preventive care and scheduling regular check-ups is a great way to catch potential health issues early and prevent gastrointestinal problems caused by parasites and systemic diseases [3]. It’s a simple step that can make a big difference in maintaining overall health and well-being.
Your dog’s gut is the foundation for digestion, immunity, skin and coat health, energy, and even behaviour. By spotting the signs of poor gut health early and making thoughtful changes, you can help your pup feel better from the inside out. When in doubt or if symptoms persist, your veterinarian is your best ally.
✅ Single ingredient, 100% pure Camelina Oil.
✅ Non-GMO
✅ Ideal balance of Omega-3 compared to other products, like soybean oil.
✅ Canadian produced and operated.
✅ Single ingredient, 100% pure Camelina Oil.
✅ Non-GMO
✅ Ideal balance of Omega-3 compared to other products, like soybean oil.
✅ Canadian produced and operated.
"Sarah is a marketing specialist with a passion for anything creative! Her openness to working across industries and job opportunities has allowed her to gain enormous amounts of experience in graphic design, video production, and written content creation. Animals have a special place in her heart as she grew up with cats and now owns her own Alaskan Malamute. She has spent the last couple of years in Vancouver working with different companies within the pet industry and gained valuable knowledge about the ins and outs of the (alternative) pet food industry, supplementation, and various training methods. When she’s not digitally creating content for pet lovers to consume, she’s out eating great food, dancing at drop-in classes, or exploring the beautiful Canadian scenery with her fur-child Miso."
