How to support your pet’s gut health when they need antibiotics

A course of antibiotics can upset the balance of your cat or dog’s gut microbiome. Here’s how to support their gut health both during and after antibiotic treatment.

Although you can’t see them, trillions of bacteria and other microbes live in and on your cat or dog, and play a critical role in nearly every aspect of their health. Although the vast majority of these microbes are beneficial, sometimes “harmful” ones, called pathogens, can lead to an infection. Your veterinarian will prescribe antibiotics to treat an infection caused by a pathogen, which can be lifesaving in some cases.

Unfortunately, antibiotics don’t just kill the bacteria causing the infection; they also harm your animal’s beneficial gut bacteria too. Many of these bacteria reside in the gut microbiome, a community of bacteria and other microbes that live in the digestive tract. A healthy and balanced gut microbiome is important for digestion, nutrient absorption, immune system function, and many other aspects of your animal’s health. Antibiotics can disturb the balance of this community, which can lead to diarrhea, vomiting, loss of appetite, and other common side effects.

Here are some simple ways you can support your cat or dog’s gut health during and after antibiotic treatment, to help mitigate any side effects and support their  recovery.

During antibiotic treatment

1. Give your cat or dog a yeast-based probiotic

Most standard probiotics are bacteria-based, and therefore susceptible to being killed by antibiotics. Yeast isn’t bacterial, so antibiotics can’t kill it. Saccharomyces boulardii, a type of yeast, is a common beneficial microbe in your animal’s gut microbial community. Studies have shown that giving S. boulardii during antibiotic treatment reduces digestive issues.

2. Encourage eating

Your animal’s diet provides him with the energy they will need to fight the infection, and the nutrition their gut bacteria need to repair and grow. A loss of appetite is a common side effect of antibiotics; when this is the case, we recommend adding warm, low-sodium, beef, chicken, or bone broth to your cat or dog’s food to make it more palatable.

After antibiotic treatment

1. Give your animal a prebiotic supplement

Prebiotics, such as psyllium husk powder or inulin, are fiber supplements that gut bacteria are able to digest. Prebiotics promote the growth of beneficial bacteria in your cat or dog’s digestive tract and help the gut microbiome rebuild after disturbances caused by antibiotic treatment.

2. Test your cat or dog’s microbiome

Microbiome testing is an easy way to determine if and what imbalances are present in your animal’s microbiome, and/or if they are missing important beneficial bacteria following antibiotic treatment. These tests often offer suggestions, such as diet recommendations, to help specific bacteria in the gut flourish.

Ongoing bacterial imbalances can sometimes lead to chronic inflammation in your cat or dog’s body, and have been linked to several health conditions that may be preventable if caught early. If a microbiome test identifies a severe bacterial imbalance, and your animal has chronic digestive issues (such as diarrhea, constipation, vomiting, etc.), they may benefit from other microbiome restoration therapies.

To learn more about your pet’s gut health visit

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Dr. Holly Ganz is a microbiologist turned entrepreneur. In 2016, she left academic research at UC Davis to create AnimalBiome, a company that provides microbiome assessments for dogs and cats and creates restorative remedies to help promote healthy guts. Dr. Ganz received her PhD from UC Davis, where she studied co-evolution between microbes and animals. Dr. Ganz is dedicated to improving animal health and wellness through applying the latest innovations in microbiology.
Katherine Dahlhausen, PhD, is a science writer for AnimalBiome. She was mentored by Holly Ganz during the beginning of her PhD at University of California Davis and helped with the very beginning of the KittyBiome project. Katherine has worked on a wide variety of microbiome-related projects to date, including ones about koalas, buildings, pollinators, and coral reefs. In her free time, she enjoys scuba diving, hiking, and cooking.