How To Support Your Dog’s Gut Microbiome During & After Antibiotics


Antibiotics can come with some negative side effects, like diarrhea and a disruption of the delicate balance of bacteria in the gut. Here are easy, science-backed tips to support dogs during and after antibiotic treatment

Antibiotics are an important tool for treating dangerous bacterial infections in dogs, but they can also come with some negative effects (like diarrhea). Antibiotics can disrupt the delicate balance of bacteria in the gut, which can lead to a range of health problems. Fortunately, there are ways that you can support your dog during and after antibiotic treatment. On a daily basis, AnimalBiome’s science team is researching and gathering data to create important tips for dog parents to use to support their pup’s gut health during and after antibiotic treatment.

How Do Antibiotics Affect Your Dog’s Gut?

The Gut Microbiome

The gut microbiome is a complex ecosystem of bacteria and other microorganisms that live in the intestines of animals. Even though they’re tiny, the microbes that live in your dog’s gut microbiome play a crucial role in digestion, immune system function, and your dog’s overall health. 

What Do Antibiotics Do?

Antibiotics kill bacteria. Your veterinarian likely prescribed an antibiotic to help treat or prevent an infection caused by a harmful bacteria. Unfortunately, antibiotics cannot differentiate between the “bad” bacteria that can cause infection and the “good” bacteria that support your pet’s health, so they wipe out both.

Common antibiotics include: amoxicillin, cephalexin, doxycycline, clindamycin, gentamicin, enrofloxacin, and penicillin. 
Common conditions antibiotics are used for include: urinary tract infections (UTIs), ear infections, respiratory infections, skin infections, and eye infections.

During Antibiotic Treatment

Tip 1: Give Your Dog The Yeast-based Probiotic S. boulardii

Saccharomyces boulardii, or S. boulardii for short, is a beneficial probiotic for dogs that can reduce inflammation and protect against the damaging effects of antibiotics. Because S. boulardii is a friendly type of yeast, it is not affected by antibiotics (which only target bacteria). Most other probiotics contain bacteria, so they’re rendered ineffective by antibiotics, too.

Studies have shown that animals are much less likely to develop diarrhea during or after a course of antibiotics when they are also given an S. boulardii supplement. For example, one study looked at healthy dogs that were given a course of antibiotics. A subset of these dogs were also given an S. boulardii supplement. None of the dogs that received an S. boulardii supplement had diarrhea, while 75% of the dogs that received antibiotics without S. boulardii had diarrhea that lasted an average of 7 days.

How Do I Pick A Probiotic That Will Work?

We get asked this a lot, and it’s true that not all probiotics are created equally. We recommend giving your pet DoggyBiome’s S. boulardii + FOS Powder.  “FOS” stands for Fructooligosaccharides, which are tiny, soluble fibers that are the preferred food of beneficial microbes like the ones we want to support in your pet’s gut. 

Studies in both cats and dogs have shown that adding FOS to the diet improves gut health. The combination of S. boulardii and FOS is proven to support beneficial bacteria during a course of antibiotics.  

Tip 2: Support A Healthy Appetite And Offer Nourishing Food

Antibiotics can cause lethargy, nausea and/or a loss of appetite, which may make your dog less interested in eating their food. It is crucial that your dog continues to eat, because their body needs the energy to continue fending off an infection and repairing damaged cells. 

If your dog refuses their food, don’t force them to eat. Here are some things you can try:

  • Wait a few hours and offer them food again
  • Add an low-sodium chicken or beef broth (without onions!) to their food to make it more palatable
  • Warm their food to bring out the aroma 
  • Try cooking a bland meal that is gentle on the tummy, such as pureed cooked chicken with a small amount of rice.

Tip 3: Finish Your Dog’s Entire Course of Treatment

It may be tempting to stop your dog’s course of antibiotics once their symptoms have gone away. However, it’s important that you finish their entire treatment to protect your dog and pets at large. 

Some infection-causing bacteria aren’t killed by antibiotics right away. They have defense mechanisms that allow them to withstand a certain amount of antibiotics, but only so much. When a course of antibiotics is finished prematurely, it creates a subpopulation of bacteria that are even stronger and more resistant to future antibiotic treatment. These stronger bacteria can be dangerous for your dog, and to other dogs they come into contact with.

Some dog parents worry about the continued damage to the microbiome by continuing with antibiotics after their dog’s symptoms improve. However, the most damage to the microbiome is caused in the first 24 hours of treatment, so the benefits of finishing the course outweigh the risks.

After Antibiotic Treatment

Tip 1: Add a Prebiotic Supplement To Your Dog’s Food

Antibiotics can significantly affect the populations of beneficial bacteria in your dog’s gut. A prebiotic supplement is a great way to naturally restore good bacteria to healthy levels. 

Prebiotics are a type of dietary fiber that are an important food source for beneficial bacteria in your dog’s gut. Inulin, psyllium husk powder, and FOS, which we mentioned earlier, have all been scientifically proven to support the growth of beneficial gut bacteria. 

Tip 2: Test For A Gut Microbiome Imbalance

Antibiotics can be very disruptive to the gut microbiome. When harmful bacteria are present or beneficial bacteria are missing, the microbiome is considered imbalanced. 

Imbalanced gut microbiomes are often associated with symptoms of chronic diarrhea, vomiting, and itchy skin, and are connected to many long-term health conditions like canine diabetes and inflammatory bowel disease

Microbiome tests are available for dogs and can be used to determine if there is an imbalance in the gut microbiome. The process is simple: you order a kit, send in a sample of your dog’s poop, and get back a comprehensive analysis of the state of your dog’s gut health. The report also includes customized dietary and supplement recommendations that take the guesswork out of how to help your dog’s gut recover from antibiotic treatment. 

Learn more about AnimalBiome’s testing science here

Tip 3: Restorative Microbiome Supplements

Sometimes gut microbiome imbalances can’t be resolved with just dietary changes or pre- and probiotic supplements. This is especially true after a course of antibiotics, when many different kinds of beneficial bacteria are affected. 

Luckily, there is a way to introduce a complete, balanced, and healthy community of microbes back to the gut. It’s called a Fecal Microbiota Transplant (FMT). Its name is self-explanatory: An FMT is the process by which stool from a healthy dog donor is delivered to the intestines of the recipient.

Some veterinarians offer FMT via enema or a nasogastric tube, but these procedures come with added risk and expense. Studies show that oral FMT capsules are just as effective at restoring the gut microbiome following antibiotic exposure.


We recommend the oral FMT capsules, DoggyBiome’s Gut Restore Supplement. The FMT material is enclosed in a specially coated capsule that allows it to pass through the stomach acid and be delivered to the intestines. The donor material is rigorously screened, as is the health of the donors.

AnimalBiome’s Perspective on Antibiotics

We believe there are instances where antibiotics are necessary, but we also believe that overuse can be dangerous to dogs. We want to empower dog parents and veterinarians alike to understand the appropriate uses of antibiotics. 
It can be harmful to prescribe antibiotics when they are not necessary. First, antibiotics are disruptive to the diversity and balance of gut microbiomes. This means that taking antibiotics when there is no infection can actually be more harmful to your dog’s health. This is especially true for animals whose gut microbiomes are already imbalanced. 
Additionally, the overuse of antibiotics leads to antibiotic resistance in all bacteria, good and bad. Not only does it reduce the global effectiveness of our existing antibiotic therapies, but antibiotic resistance also leads to the emergence of dangerous ‘superbugs’ (pathogens resistant to all known antibiotic therapies).
We encourage veterinarians to use an antimicrobial stewardship approach, and encourage pet parents to discuss this topic with their veterinarian. This includes stepping away from the common practice of prescribing antibiotics to prevent infections that may not occur anyway, and only prescribing antibiotics when a bacterial infection is confirmed. 

Questions For Your Veterinarian

Does my dog really need antibiotics or is there an alternative treatment we can try?

What are the common side effects of antibiotics and how should I care for my dog if they experience them?

Will giving antibiotics with food help decrease the chance of nausea?

How long will my dog be on antibiotics?

Are there certain antibiotics that are easier on my dog’s gut?

Interested in Learning More? 

Keep Reading 

Has Your Dog Been Prescribed Metronidazole? Important Information All Owners Should Know

1 in 3 Dog Guts Have Too Much E. coli: Symptoms and Solutions

Get in Touch

Our team of scientists is dedicated to the health and wellbeing of companion animals. We’d love to help you find effective solutions for your dog’s microbiome health. Get in touch with us at team@animalbiome.com to find out where to start.

If you found this article helpful, please consider sharing it.


Suggested Products



How To Support Your Dog’s Gut Microbiome During & After Antibiotics


Antibiotics can come with some negative side effects, like diarrhea and a disruption of the delicate balance of bacteria in the gut. Here are easy, science-backed tips to support dogs during and after antibiotic treatment

Antibiotics are an important tool for treating dangerous bacterial infections in dogs, but they can also come with some negative effects (like diarrhea). Antibiotics can disrupt the delicate balance of bacteria in the gut, which can lead to a range of health problems. Fortunately, there are ways that you can support your dog during and after antibiotic treatment. On a daily basis, AnimalBiome’s science team is researching and gathering data to create important tips for dog parents to use to support their pup’s gut health during and after antibiotic treatment.

How Do Antibiotics Affect Your Dog’s Gut?

The Gut Microbiome

The gut microbiome is a complex ecosystem of bacteria and other microorganisms that live in the intestines of animals. Even though they’re tiny, the microbes that live in your dog’s gut microbiome play a crucial role in digestion, immune system function, and your dog’s overall health. 

What Do Antibiotics Do?

Antibiotics kill bacteria. Your veterinarian likely prescribed an antibiotic to help treat or prevent an infection caused by a harmful bacteria. Unfortunately, antibiotics cannot differentiate between the “bad” bacteria that can cause infection and the “good” bacteria that support your pet’s health, so they wipe out both.

Common antibiotics include: amoxicillin, cephalexin, doxycycline, clindamycin, gentamicin, enrofloxacin, and penicillin. 
Common conditions antibiotics are used for include: urinary tract infections (UTIs), ear infections, respiratory infections, skin infections, and eye infections.

During Antibiotic Treatment

Tip 1: Give Your Dog The Yeast-based Probiotic S. boulardii

Saccharomyces boulardii, or S. boulardii for short, is a beneficial probiotic for dogs that can reduce inflammation and protect against the damaging effects of antibiotics. Because S. boulardii is a friendly type of yeast, it is not affected by antibiotics (which only target bacteria). Most other probiotics contain bacteria, so they’re rendered ineffective by antibiotics, too.

Studies have shown that animals are much less likely to develop diarrhea during or after a course of antibiotics when they are also given an S. boulardii supplement. For example, one study looked at healthy dogs that were given a course of antibiotics. A subset of these dogs were also given an S. boulardii supplement. None of the dogs that received an S. boulardii supplement had diarrhea, while 75% of the dogs that received antibiotics without S. boulardii had diarrhea that lasted an average of 7 days.

How Do I Pick A Probiotic That Will Work?

We get asked this a lot, and it’s true that not all probiotics are created equally. We recommend giving your pet DoggyBiome’s S. boulardii + FOS Powder.  “FOS” stands for Fructooligosaccharides, which are tiny, soluble fibers that are the preferred food of beneficial microbes like the ones we want to support in your pet’s gut. 

Studies in both cats and dogs have shown that adding FOS to the diet improves gut health. The combination of S. boulardii and FOS is proven to support beneficial bacteria during a course of antibiotics.  

Tip 2: Support A Healthy Appetite And Offer Nourishing Food

Antibiotics can cause lethargy, nausea and/or a loss of appetite, which may make your dog less interested in eating their food. It is crucial that your dog continues to eat, because their body needs the energy to continue fending off an infection and repairing damaged cells. 

If your dog refuses their food, don’t force them to eat. Here are some things you can try:

  • Wait a few hours and offer them food again
  • Add an low-sodium chicken or beef broth (without onions!) to their food to make it more palatable
  • Warm their food to bring out the aroma 
  • Try cooking a bland meal that is gentle on the tummy, such as pureed cooked chicken with a small amount of rice.

Tip 3: Finish Your Dog’s Entire Course of Treatment

It may be tempting to stop your dog’s course of antibiotics once their symptoms have gone away. However, it’s important that you finish their entire treatment to protect your dog and pets at large. 

Some infection-causing bacteria aren’t killed by antibiotics right away. They have defense mechanisms that allow them to withstand a certain amount of antibiotics, but only so much. When a course of antibiotics is finished prematurely, it creates a subpopulation of bacteria that are even stronger and more resistant to future antibiotic treatment. These stronger bacteria can be dangerous for your dog, and to other dogs they come into contact with.

Some dog parents worry about the continued damage to the microbiome by continuing with antibiotics after their dog’s symptoms improve. However, the most damage to the microbiome is caused in the first 24 hours of treatment, so the benefits of finishing the course outweigh the risks.

After Antibiotic Treatment

Tip 1: Add a Prebiotic Supplement To Your Dog’s Food

Antibiotics can significantly affect the populations of beneficial bacteria in your dog’s gut. A prebiotic supplement is a great way to naturally restore good bacteria to healthy levels. 

Prebiotics are a type of dietary fiber that are an important food source for beneficial bacteria in your dog’s gut. Inulin, psyllium husk powder, and FOS, which we mentioned earlier, have all been scientifically proven to support the growth of beneficial gut bacteria. 

Tip 2: Test For A Gut Microbiome Imbalance

Antibiotics can be very disruptive to the gut microbiome. When harmful bacteria are present or beneficial bacteria are missing, the microbiome is considered imbalanced. 

Imbalanced gut microbiomes are often associated with symptoms of chronic diarrhea, vomiting, and itchy skin, and are connected to many long-term health conditions like canine diabetes and inflammatory bowel disease

Microbiome tests are available for dogs and can be used to determine if there is an imbalance in the gut microbiome. The process is simple: you order a kit, send in a sample of your dog’s poop, and get back a comprehensive analysis of the state of your dog’s gut health. The report also includes customized dietary and supplement recommendations that take the guesswork out of how to help your dog’s gut recover from antibiotic treatment. 

Learn more about AnimalBiome’s testing science here

Tip 3: Restorative Microbiome Supplements

Sometimes gut microbiome imbalances can’t be resolved with just dietary changes or pre- and probiotic supplements. This is especially true after a course of antibiotics, when many different kinds of beneficial bacteria are affected. 

Luckily, there is a way to introduce a complete, balanced, and healthy community of microbes back to the gut. It’s called a Fecal Microbiota Transplant (FMT). Its name is self-explanatory: An FMT is the process by which stool from a healthy dog donor is delivered to the intestines of the recipient.

Some veterinarians offer FMT via enema or a nasogastric tube, but these procedures come with added risk and expense. Studies show that oral FMT capsules are just as effective at restoring the gut microbiome following antibiotic exposure.


We recommend the oral FMT capsules, DoggyBiome’s Gut Restore Supplement. The FMT material is enclosed in a specially coated capsule that allows it to pass through the stomach acid and be delivered to the intestines. The donor material is rigorously screened, as is the health of the donors.

AnimalBiome’s Perspective on Antibiotics

We believe there are instances where antibiotics are necessary, but we also believe that overuse can be dangerous to dogs. We want to empower dog parents and veterinarians alike to understand the appropriate uses of antibiotics. 
It can be harmful to prescribe antibiotics when they are not necessary. First, antibiotics are disruptive to the diversity and balance of gut microbiomes. This means that taking antibiotics when there is no infection can actually be more harmful to your dog’s health. This is especially true for animals whose gut microbiomes are already imbalanced. 
Additionally, the overuse of antibiotics leads to antibiotic resistance in all bacteria, good and bad. Not only does it reduce the global effectiveness of our existing antibiotic therapies, but antibiotic resistance also leads to the emergence of dangerous ‘superbugs’ (pathogens resistant to all known antibiotic therapies).
We encourage veterinarians to use an antimicrobial stewardship approach, and encourage pet parents to discuss this topic with their veterinarian. This includes stepping away from the common practice of prescribing antibiotics to prevent infections that may not occur anyway, and only prescribing antibiotics when a bacterial infection is confirmed. 

Questions For Your Veterinarian

Does my dog really need antibiotics or is there an alternative treatment we can try?

What are the common side effects of antibiotics and how should I care for my dog if they experience them?

Will giving antibiotics with food help decrease the chance of nausea?

How long will my dog be on antibiotics?

Are there certain antibiotics that are easier on my dog’s gut?

Interested in Learning More? 

Keep Reading 

Has Your Dog Been Prescribed Metronidazole? Important Information All Owners Should Know

1 in 3 Dog Guts Have Too Much E. coli: Symptoms and Solutions

Get in Touch

Our team of scientists is dedicated to the health and wellbeing of companion animals. We’d love to help you find effective solutions for your dog’s microbiome health. Get in touch with us at team@animalbiome.com to find out where to start.

If you found this article helpful, please consider sharing it.


Suggested Products


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