How To Manage Dog Diarrhea After Antibiotics

antibiotic damage
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Our dogs are walking, barking ecosystems.  

Like you, your dog is carrying trillions of other organisms around in his body. These little guys outnumber the cells in the body 10:1. This group of bacteria, fungi, archaea, and eukaryotes make up the canine microbiome. They’re nestled in your dog’s nail-beds, gathered in his gut, and spread all over his skin, lungs and urinary tract.

The canine microbiome helps protect against disease, maintain healthy digestion and regulate hormones. So, a healthy microbiome = a healthy dog. But what happens when you add the side effects of antibiotics in dogs into the equation? What can you do to prevent and manage dog diarrhea after antibiotics?

Canine Dysbiosis And Disease

The latest research shows what we already know about our own microbiomes is true for dogs too (1). Dysbiosis is what happens when the canine microbiome is out of balance. There’s tons of evidence linking an imbalanced microbiome to a variety of diseases:

1. Obesity

Obesity is a fast-spreading epidemic among both humans and pets. It affects up to 50% of dogs … and can cause a bunch of different issues. The microbiome of obese dogs is less diverse than healthy dogs. 

There’s evidence that improving the microbiome of overweight dogs can help weight loss (2).

2. Mental Health

It’s now known that the dog’s microbiome and central nervous system “talk” all the time. And this chatter has a profound impact on the mental state. This can cause stress, anxiety, depression and cognitive dysfunction. New research has focused in on a link between aggression and dysbiosis (3)

3. Cancer

Dysbiosis has been linked to the development of several different cancers … such as intestinal lymphoma (4).

4. Exocrine Pancreatic Insufficiency (EPI)

A diseased pancreas does a very bad job at digesting food in the intestines. One study has shown that dogs with EPI often have dysbiosis (5).

5. Inflammatory Bowel Disease (IBD)

The microbiome supports your dog’s immune system. In the gut, it does this by helping to fend off intruders. New evidence shows that it also destroys sick immune cells that can cause diseases like IBD.

6. Infections

A healthy microbiome fends off disease. A dysfunctional microbiome leaves your dog vulnerable to nasty infections.

7. Diarrhea

Diarrhea often comes from an imbalance in the microbiome of the gut. Feeding processed foods, disease and antibiotics weaken the microbiome. This can allow disease-causing organisms to flourish. So to manage dog diarrhea after antibiotics, keep reading …

With many of these health conditions, conventional veterinarians reach for antibiotics …

RELATED: What are the best probiotics for dogs?

Antibiotic Damage To The Microbiome

Antibiotics have the same effect on the microbiome as bulldozers in a rainforest. A few organisms in the microbiome are resistant to some common antibiotics. Many are not. Killing the beneficial organisms exposes your dog to a host of diseases.

We’ve learned that antibiotics can be detrimental to the health of your dog’s microbiome. If this is the case … why should we use them at all?

Veterinarians are under increasing pressure to prescribe antibiotics with extra care. Unfortunately, drug companies feed a lot of misleading information to vets. Combined with pressure from peers, this leads a lot of vets to over-use antibiotics. In fact, the American Veterinary Medical Association’s (AVMA) Task Force For Antimicrobial Stewardship in Companion Animals said it “seems likely” that the amount of unnecessary use of antibiotics in companion animal settings is close to 50% .

Massive antibiotic misuse has led to the development of antibiotic-resistant organisms. These organisms continue to flourish even when treated with our strongest medicines. There are even concerns that otherwise healthy dogs carry and spread these bugs.

There’s a chance that some day your dog will come across a disease that his immune system can’t fight off. It’s important to use antibiotics sparingly, and only when they’re really necessary. Always make an informed decision when it comes to antibiotic use in your dog. Where the situation is not life-threatening, consider other options.

Be sure to make it clear to your veterinarian that you would prefer to avoid unnecessary antibiotic use. There are many natural alternatives that won’t cause the same damage to your dog’s health.

But it isn’t just antibiotics that can harm these beneficial organisms. Your dog’s microbiome is also sensitive to other drugs and foods. One example is a proton pump inhibitor drug called omeprazole. This drug helps suppress stomach acid, in both humans and dogs. While further studies are needed, this drug has already been linked to dysbiosis (6).

Rebuilding The Canine Microbiome

So, what can you give a dog for upset stomach from antibiotics? Here are some handy tips to help protect your dog from antibiotic damage … and restore his gut health after antibiotics.

1. What To Feed Dog On Antibiotics

A raw diet (aka a high protein low carb – HPLC) diet improves diversity in the gut microbiome. Some studies have even shown knock-on effects with obesity. Beagles and Labradors lost weight … while minimizing muscle loss … on a HPLC diet supplemented with fiber (7).

The most important thing to prevent dysbiosis is to avoid dry food … (yes, that means kibble) … which is always high in carbohydrate. A raw, fresh food diet can promote a more balanced gut microbiome. Balanced and nutritious high protein, low carb, raw food is usually the best diet for your dog. After all, dogs don’t need carbs.

2 Give Your Dog Probiotics

To rebuild the canine microbiome … feed a probiotic that contains a wide variety of bacteria, with a high number of organisms. Probiotics balance outl disease-causing organisms, and replace dwindling numbers of good organisms. If you buy a probiotic, the best type of probiotic includes soil-based organisms that are spore forming and can survive antibiotic damage (9, 10). S. boulardii, a probiotic yeast, has also been shown to be effective in resolving dog diarrhea after antibiotics (11).

You can also feed probiotic foods like kimchi and fermented veggies.

And, don’t forget to feed the probiotics with prebiotics. Prebiotics are a type of dietary fiber that help feed the microbiome in the gut. Studies show that prebiotics help improve digestion in our dogs. Some great natural sources of prebiotics include bananas, dandelion greens, and asparagus.

Occasionally antibiotics may be unavoidable. If so, pre and probiotics are really, really important for helping rebuild gut health.

DNM RECOMMENDS: Four Leaf Rover offers Protect, a veterinarian-formulated soil-based probiotic blend containing spore-forming bacteria species and S. boulardii to protect and restore the gut from antibiotic damage. Buy Protect now >>

3. Try A Fecal Transplant

Fecal transplantation is exactly what it sounds like. Transplanting poop.

More specifically … it involves transplanting fecal matter from a healthy dog to an unhealthy dog. In humans, this type of therapy has shown amazing results … helping with everything from Clostridium difficile infections to Crohn’s disease. In animals, fecal transplants can treat things like digestive issues and autoimmune disease (12). They’re especially useful for rebuilding the gut after antibiotics have damaged it. Several holistic vets perform fecal transplants in dogs.

RELATED: Find out about fecal transplant in dogs …

Why does my dog have diarrhea after taking antibiotics?

Your dog’s digestive health relies on the balance of good bacteria in his gut. Antibiotics kill bacteria, so when you give antibiotics, they destroy all gut bacteria, good and bad … often creating long-lasting damage to your dog’s gut and immune health.

How long does diarrhea last in dogs after antibiotics?

Every dog is different in how they respond, but research shows that antibiotics can cause long-term gut damage … some research has found the effects last up to 2 years. Research at NYU Langone Medical Center found “Early evidence … hints that, sometimes, our friendly flora never fully recover.”

How can I restore my dog’s gut after antibiotics?

To help your dog recover from antibiotic damage, feed a raw, whole food diet, and give probiotics with soil-based organisms and S. boulardii, a probiotic yeast that has been shown to heal the gut after antibiotics.

Your dog’s microbiome is amazing. It’s a very important asset in the fight against disease. To keep your dog healthy and happy, you need to pay attention to gut health and do everything you can to keep it in check.

  1. Coelho, L.P., Kultima, J.R., Costea, P.I. et al. Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome 6, 72 (2018)
  2. Kieler IN, Shamzir Kamal S et al. Gut microbiota composition may relate to weight loss rate in obese pet dogs. Vet Med Sci. 2017;3(4):252-262. Published 2017 Nov 3.
  3. Kirchoff NS, Udell MAR, Sharpton TJ. 2019. The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris). PeerJ 7:e6103
  4. A Gavazza et al. Faecal microbiota in dogs with multicentric lymphoma. Vet Comp Oncology. March 2018.
  5. Anitha Isaiah et al. The fecal microbiome of dogs with exocrine pancreatic insufficiency. Anaerobe, Volume 45, 2017
  6. Kostrzewska M et al. The effect of omeprazole treatment on the gut microflora and neutrophil function. Clin Res Hepatol Gastroenterol. 2017 Oct;41(5):575-584.
  7. Li Q, Lauber CL et al. Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions. mBio. 2017;8(1):e01703-16. Published 2017 Jan 24.
  8. Becattini S, Taur Y, Pamer EG. Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. Trends Mol Med. 2016 Jun;22(6):458-478. 
  9. Thiemann S, Smit N, Strowig T. Antibiotics and the Intestinal Microbiome : Individual Responses, Resilience of the Ecosystem, and the Susceptibility to Infections. Curr Top Microbiol Immunol. 2016;398:123-146. 
  10. Pamer EG. Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens. Science. 2016;352(6285):535-538.
  11. Blaabjerg S, Artzi DM, Aabenhus R. Probiotics for the Prevention of Antibiotic-Associated Diarrhea in Outpatients-A Systematic Review and Meta-Analysis. Antibiotics (Basel). 2017;6(4):21. Published 2017 Oct 12.
  12. Surawicz CM, Elmer GW, Speelman P, McFarland LV, Chinn J, van Belle G. Prevention of antibiotic-associated diarrhea by Saccharomyces boulardii: a prospective study. Gastroenterology. 1989 Apr;96(4):981-8.
  13. Chaitman J, Gaschen F. Fecal Microbiota Transplantation in Dogs. Vet Clin North Am Small Anim Pract. 2021 Jan;51(1):219-233. 


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