How to Protect Your Dog's Gut Health While on Antibiotics [Easy!] Antibiotics are medicines that inhibit or stop the growth of microorganisms (bacteria).  But, unfortunately, antibiotics are indiscriminate.   They don’t play favorites.  They not only kill the bad bacteria, like those potentially inside Junior’s lump, but they also kill the good bacteria in his gut.  The technical term for this microbial imbalance is dysbiosis.
/ How to Protect Your Dog’s Gut Health While on Antibiotics [Easy!]

How to Protect Your Dog’s Gut Health While on Antibiotics [Easy!]

Nutritional Supplements and Medications For Dogs

Big Dog Ailments

The impact of your dog’s gut health is far-reaching.

Let’s look at the following common ailments of large breed dogs:

  • Chin acne
  • Diarrhea
  • Ear Infections

What these have in common is the necessity of antibiotics to heal them.  And each time antibiotics are given, your dog’s gut health suffers.

Would you like to know how to prevent that damage and ensure your dog not only fights the infection but comes out the other end even stronger?

If so, stick with me and I will show you how!

Junior and the Battle Within

Gut Health on Antibiotics

As I mentioned in The Ultimate Guide to Saving Money on Pet Medications, Junior has a painful lump on his shoulder which my vet theorizes is an abscess caused by a vaccine he was given several months ago.

Because abscesses are usually infections filled with bacteria, we are attempting to “kill” this abscess using a very strong antibiotic called Clindamycin.   Junior will continue taking three large 300 mg capsules twice a day for another month before we determine whether surgery will be necessary.

Prayers appreciated.

Given the severity of Junior’s condition and the length (and strength) of antibiotic treatment he is on, my primary focus right now is boosting his immune system.

On behalf of my poor Junior’s embattled immune system, I sought answers.

Big Dog Mom to the rescue!


This post contains affiliate links from which I may receive a small compensation.  There is NO ADDED COST to you should you use these links.


What is Gut Health?

The gut is another word for the gastrointestinal system, gastrointestinal tract, digestive system, or digestive tract.  It is a group of organs that includes the mouth, esophagus, stomach, pancreas, liver, gallbladder, small intestine, colon, and rectum.

Within the gut, according to Dog’s Naturally Magazine, is what is referred to as “gut-associated lymphoid tissue” or GALT, which is the largest immune organ in the body. 

This lymphoid tissue lining the gut wall combines with other immune components within the gut including the mucosal lining,  the probiotics (good bacteria) and microbiome (a mini-ecosystem in the gut), and a wealth of antigens that have been produced by specialized cells lining the gut.

It is believed that GALT and its associated entities may contribute up to a whopping 70 percent of your dog’s total immune capability.

A logical analogy seems appropriate here:

Man’s Heart : His Stomach :: Dog’s Immune System : His Gut.

Gut Health on Antibiotics

“Am I a dog, that you should come at me with sticks?” ~ Goliath

So, what happens to your dog’s gut health when he is on an antibiotic?

Antibiotics are medicines that inhibit or stop the growth of microorganisms (bacteria).  But, unfortunately, antibiotics are indiscriminate.   They don’t play favorites.  They not only kill the bad bacteria, like those potentially inside Junior’s lump, but they also kill the good bacteria in his gut.  The technical term for this microbial imbalance is dysbiosis.

This is the caricature going on in my head:

Maintaining gut health while taking antibiotics is like a tug of war between David and Goliath in the Valley of Elah.

Clindamycin and the lump requiring it (aka Goliath) take one look at the tiny pee wee microbes (David) in Junior’s gut and laugh.  “Am I a dog that you should come at me with sticks?” Goliath chastises.

(You know you have small children when brilliant analogies come in the form of animations.)

Like David, against serious illness and a powerful antibiotic, Junior’s gut bacteria are the clear underdogs (no pun intended).

Please follow this list of DO’s and DON’Ts when it comes to preserving gut health while your dog is taking antibiotics.  Doing so will ensure David walks away the victor.

Maintaining gut health while taking antibiotics is like a tug of war between David and Goliath in the Valley of Elah. Click to Tweet

Gut Health Do’s

1. Supplement with Probiotics

Probiotics are live microorganisms (i.e. good bacteria) that, when fed in adequate amounts, provide a health benefit to your dog.

With trillions and trillions of microorganisms in his body, from over 1,000 different strains of bacteria,  researchers believe as much as 70% of your dog’s immune system is based in his gut.  The ratio of “good” bacteria to “bad” bacteria existing in the intestines has a direct impact on how well your dog’s immune system fights off infections and diseases.

Because antibiotics are doing their best to wipe out these friendly florae, it is critical that we add them back in through supplementation.

Variety is best.  I use and have used several probiotic supplements over the last year which I will provide here as options for you to consider.

Among these are NWC Naturals Total-Biotics, which delivers 1 billion CFU’s (colony forming units) of 14 different strains of bacteria per scoop, TummyWorks™Nusentia Probiotic Miracle, kefir, and plain yogurt.   Fermented vegetables, bone broth, and raw goat’s milk are also great options as well.

[READ: All Natural Pet Supplements for Big Dogs – A Review of Finest For Pets for a full review of TummyWorks™]

I give Junior and Sulley probiotics on a daily basis.  When they are on an antibiotic though, I increase not only the amount I give but the variety and frequency as well.   In addition to the Nusentia Probiotic Miracle that I am giving now, I also give Junior and Sulley a complementary enzyme supplement (NWC Naturals Total-Zymes) which provides 16 different enzymes including digestive enzymes and prebiotics.

For a comprehensive dive into probiotics for dogs, read Probiotics for Dogs: The Facts and Strains that Matter Most

2. Don’t Forget Your Prebiotics

These are the food for the probiotics.

Prebiotic fiber is the non-digestible part of foods like certain vegetables and fruits.  Prebiotics move through the small intestine undigested and are fermented when they reach the colon.

This fermentation process feeds beneficial bacteria colonies (including probiotic bacteria) and helps to increase the number of desirable bacteria in your dog’s gut that are associated with better health, a stronger immune system, and reduced disease risk.

Many probiotic supplements include some prebiotics in them.  All three of the supplements I mentioned earlier include one or more prebiotics to feed the growth of the accompanying probiotics.

I also feed Junior and Sulley fruits like bananas and apples in small amounts which serve as a whole food prebiotic.

3. Refrigerate Your Probiotic Supplement

Gut Health on Antibiotics for Dogs Infographic

Refrigeration, and in some cases freezing, will extend the shelf life of your probiotic. 

Bacteria are naturally sensitive to heat and moisture, so keeping them stored in a cool, dry place is key to maximizing the gut health benefit you get from them.

4. Inoculate Your Probiotic

In order to extend the life of your probiotic supplement, consider inoculating it into a medium like milk, raw goat’s milk preferably. 

The benefit of doing this is that just one or two scoops of your probiotic will grow and reproduce in the milk, effectively doubling or tripling (or more) the amount that you have to give.

5. Feed the Antibiotic with Food

While your probiotics will help with digestive upset, feeding an antibiotic on an empty stomach can cause your dog some gut distress.

Keep in mind this is a general rule, not specific to every antibiotic.  You will want to check with your veterinarian or pharmacist for guidance.

Gut Health Don’ts

1. Feed Probiotics and Antibiotics Together!

Let me illustrate why.

Picture this…

Goliath steps up to the battle line and snatches the 5 smooth stones in David’s bag before David has the opportunity to clock Goliath in the head with them.

If given together, the antibiotic will essentially wipe out the bacteria in your probiotic before this friendly flora has a chance to benefit your dog’s gut health.

A good general rule is to SEPARATE the antibiotic from your probiotic supplementation by about TWO HOURS.

If given together, the antibiotic will essentially wipe out the bacteria in your probiotic before this friendly flora has a chance to benefit your dog’s gut health. Click to Tweet

2. Ignore the Importance of Your Dog’s Diet.

A diet of exclusively dry kibble is not doing your dog’s gut health any favors, particularly when he is on an antibiotic.

Let me explain.

If your dog has a serious illness, like one requiring an antibiotic, his immune system will be less able to fight it with grain-filled food.

The reason is simple and it has to do with carbohydrates.

Dogs’ digestive tracts are short and designed for quickly digesting animal protein and fat, but not carbohydrates. Complex carbohydrates like those found in grains and starches are very difficult to digest and absorb. And as your dog’s body tries to digest them, his metabolism becomes less efficient and his immune system is similarly weakened.

Watch this video entitled The Unknown Sugar In Pet Food produced by Dr. Karen Becker, DVM and Rodney Habib of Planet Paws.   They do a terrific job illustrating the extent to which carbohydrates make up a commercial kibble diet and how this excess sugar contributes to common health problems in dogs.

By contrast, the digestive enzymes and bacteria found in fresh (raw) food help dogs digest food better and build stronger immune systems. These necessary nutrients are not found in processed foods, as the processing and cooking destroy them.

If you are interested in learning more about raw feeding, read:

3. Waste Your Money

In addition to inoculating and refrigerating your probiotic, in my last post, The Ultimate Guide to Saving Money on Pet Medications, I outline numerous ways to save money on medications such as antibiotics.

I don’t know about you, but we live on a budget. As often as I say I would pay ANY amount of money to ensure my dogs are happy and healthy, I am not willing to OVERpay for it.

Gut Health Summary

Combining a raw, species-appropriate diet with healthy, timely, supplementation of probiotics and prebiotics, give your dog’s gut health the boost it desperately needs to fight the battle within.

The immune system victory against an adversary like Goliath will require more than “sticks” or stones.

It will require the collective power of billions of microbes, the friendly flora, to bring the microbiome in your dog’s gut back into balance.

Gut Health Must Have Resources

Probiotics for Dogs: The Facts and Strains that Matter Most

Dog’s Naturally Magazine

Calculating Pet Food Dry Matter Basis  This is a terrific article I found that illustrates exactly HOW to calculate the % of carbohydrates in your dog’s food.

Similar Posts

43 Comments

  1. Excellent information! As usual, you do the research and I will listen?
    Both of my Rhodesian Ridgebacks should be on Probiotics. Thank you for your insight!

    1. Aww, thank you Fran! I hope everything is ok with your Ridgebacks. I am always here to help if you need me!

  2. Great post with lots of important information. Probiotics are important for humans so it makes sense that they are important for our pets too. The Dos and Don’ts are especially helpful.

    1. Thank you so much! Yes, I try and take a probiotic, whether in the form of a whole food source or supplement, everyday.

  3. I am a bid gab of probiotics. Both of my dogs use them.

    1. That’s wonderful, Carleen! Your dogs will be healthier by adding this simple supplement to their diet.

  4. Everything you wrote is what my vet told me when Layla was on antibiotics and it made so much sense to me, now reading your post is making me feel better cos all I worried about was nutrition and he told me to stop worrying – thanks

    1. That is wonderful to hear! Thank you! It’s no fun to have a dog that isn’t well and having to be on antibiotics. It is even worse when we have to worry about their nutrition on top of it.

  5. Probiotics has never been an avenue I went down with my dogs, but this makes me want to reconsider. Thanks for such an informative post.

    1. Thank you, Jill! Yes, I would absolutely reconsider giving probiotics. I give them daily in one form or another.

  6. Mr. N has a delicate stomach so he takes probiotics. He’s tiny so it doesn’t take much. After almost a year, we’re about done with a jar.

    1. Wow! A year is a long time. I will say since the scoops are so small I go through a container probably every other month if not quarterly. They really are a very economical supplement comparatively speaking.

  7. We use antibiotics very rarely but when we must, we too take measures to protect the gut flora.

    1. Good for you, Jana! Yes, I try to avoid antibiotics when possible. Unfortunately, they are necessary sometimes.

  8. Such great information! I knew that if your pet uses antibiotics, that you should give probiotics, but I didn’t know about the timing difference and my vet never mentioned it. I also like the idea of infusing the milk and getting more probiotics.

    I’ve only used probiotics when Buffy gets an upset tummy for a few days. I have not tried pre-biotics. I’ll have to give her more pieces of banana and apples.

    I look forward to reading more informative posts.

    1. Thank you so much, Sandy! I’m thrilled the information was helpful for you and Buffy. Junior and Sulley love apples and bananas so offering a prebiotic source is pretty easy for us thankfully. Prebiotics are also often added with many probiotic supplements and enzyme supplements as well for dogs that don’t eat veggies and fruit.

  9. Elizabeth says:

    Probiotics are always a good thing! We recommend them to clients at the clinic all the time, especially with antibiotics. (I’m a vet tech)

  10. Plenty of great information here to keep a dog owner happy and well informed!

    Our Humarian probiotics don’t need refrigerating which is the only big difference on our gut health regimen for the cats. (Just as well because I would forget and leave them out all day = ruined * sigh *)

    I hope Junior’s access resolves on its own and you don’t need surgery. Good luck.

    1. Thank you so much! That is interesting about the Humarian probiotics. I’m researching now for a future post on probiotics, so I will have to look at yours.

  11. When my dog was on probiotics and antibiotics, my vet didn’t mention that they needed to be given at different times. Luckily, my mom takes probiotics and I learned a lot from her. Probiotics make a huge difference for both my mom and my dogs when they are on antibiotics.

    1. Hi Beth – yes, my vet never mentioned this either. It seems to me that this would be one of the very basic things they tell pet owners, but, sadly, I have never been recommended to give a probiotic either. :/

  12. I use probiotics with my cats’ raw diet, but I learned a lot from this post. My probiotics are going in the fridge right now. The idea of adding it to milk I never would have thought of doing.

  13. Great post as always! Luckly, we never had to use antibiotics with our cat. She is one healthy kitty! Hope it will stay that way 🙂

    1. Yes, I do hope you never need to use them on your kitty! Thank you!

  14. Although I don’t have any dogs this information is super helpful! I’m sure other dog mom’s experiencing the same thing will appreciate your tips. Will share!

  15. Our cat Charlie developed a lump from her distemper vaccine. We weren’t prescribed antibiotics but it did go away, eventually. It makes sense to try to protect the good bacteria while eliminating the bad. I didn’t know own there were probiotics for dogs. Henry is a little dog with huge digestive issues. The raw diet seemed to help but I will still try probiotics for him. They’re part of my (human) routine. Thanks for the information!

  16. At some point we should compare all of our favorite resources because you and I read/follow so many of the same experts. Just another reason I love reading your blog. I get to see how another dog mom implements the advice. This post is especially helpful. Bernie and Lizzie both take probiotics, usually with breakfast. Lizzie had a UTI a few weeks ago, so I switched the timing of the probiotic to dinner so it wouldn’t coincide with the “every 12 hours” direction on the antibiotic. Thank you for the link on calculating carbs in kibble. I’ve got the pups on an organic non-GMO kibble, which is the highest quality kibble I could find. I am curious what the percent carbs is. I supplement their meals with cooked protein and raw veggies and fruits, but I really wish I could feed them raw.

    1. I agree, Irene! I am interested in what you find when you do the calculations on carb content for your food. Ideally you would eventually be able to transition Bernie and Lizzie to raw, but the fact that you are providing them some raw, natural food sources is great. You might consider seeking advice from other folks with dogs that have Addison’s Disease and see who is feeding raw and how that is working for them. Because I have no experience with this condition, I am in no position to recommend a switch. My guess is the small additions of whole foods, plus the probiotics, are providing health benefits as it is. You will have to let me know if and when you decide to give raw a try. I’d love to share your experience on Big Dog Mom. 🙂

  17. Excellent post full of excellent information. I’m so happy to see prebiotics here as well. Such an important point (for us humans, too). I have included probiotics as part of my Huskies daily diet for many years per advice of one of my vets. When my one girl was on antibiotics for a repeat ear infection (ugh, poor girl), I am sure to boost her immune system as well. I’ve Pinned this over on my “Bark About” board to keep in my library and to share as well!

    1. Thank you so much, Dorothy! Yes, probiotics without the prebiotics (food to feed them) are limited in their benefit. My supplements all include a prebiotic, but I also add some sliced apple and banana a few times a week as well because they are a great prebiotic source and the boys love them. Thank you so much for pinning this!

  18. Not sure if you have been following but people are using fecal transplants similar to using probiotics/prebiotics to get the microbiome back to normal to kill bacteria like c Diificile as an alternative to antibiotics and to cure a lot of stuff. My kids both have issues.

    1. Hummmm, I will have to do some research on this! Thank you so much for the information! I will check it out for sure.

  19. I know the importance of probiotics because my doctor has me on them because of my Celiac disease. The girls aren’t aren’t any probiotics at the time. I’m a little surprised the vet didn’t recommend them after Truffle’s surgery and an affection that occurred two weeks later. She was on antibiotics for several weeks.

    1. As much as I love my vet and respect her advice, I don’t wait for her to recommend anything as it relates to their diet or nutrition/supplements. I just know there is a limit to her knowledge and expertise. She is supportive of me feeding raw, and when I told her I was giving a probiotic, she said it was fantastic and very good for my dogs. That said, she was not the one who recommended I do it. So, my recommendation is to start Brulee and Truffle on a probiotic, especially Truffle given her surgery and antibiotic use recently. There is a ton of research out there about giving probiotics to cats if you are unsure. Good luck!

  20. The last time Icy had tummy issues, which thankfully was a long time ago, our Vet gave her both an antibiotic and a probiotic to take with it to counteract the gut effects of the antibiotic.
    Love & Biscuits,
    Dogs Luv Us and We Luv Them

    1. Wow! I’m pleasantly surprised your vet gave her a probiotic as well. That’s wonderful!

  21. This is great information on gut health for dogs! I like to give my dogs raw goat milk when they need probiotics. I also use Nupro supplement that helps improve immunity.

    1. Thank you so much! I give Nupro to Junior and Sulley as well. 🙂

  22. I live in a very remote area and don’t have access to a lot of foods I have two huskies that keep getting dermatitis issues and Antibiotics are making them sick, is there anything that I could have in my cupboard that you would suggest that might help there bellies? I would appreciate any help you could give me

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.