by Narelle Cooke, Canine Nutritionist

Just like humans, our dogs can fall ill and require medical treatment, including the use of antibiotics. Antibiotics, derived from the Greek words "anti" (against) and "bios" (life) are essential for tackling harmful bacteria that can lead to various conditions, from gastrointestinal infections to respiratory issues. But while antibiotics are effective in wiping out disease-causing bacteria, they also disrupt the delicate balance of the gut microbiome - home to billions of beneficial microorganisms crucial for digestion, nutrient absorption, and immune function – which can lead to a condition called dysbiosis.1 Intestinal imbalance can continue for many weeks to months after stopping antibiotic therapy, and in some cases, the gut never fully reverts back to its original state.2 This imbalance may make dogs more susceptible to gastrointestinal issues, allergies, and even potential future infections.  As a result, maintaining gut health during and after antibiotic treatment is vital for your dog's overall well-being. Fortunately, there are proactive steps we can take to support our dogs in restoring a balanced gut microbiome.

Do’s and Don’ts - During antibiotic treatment

Do …. Supplement with the probiotic species Saccharomyces boulardii

Unlike most commercially available probiotics that are bacteria-based and thus susceptible to being eradicated by antibiotics, Saccharomyces boulardii is a beneficial yeast that remains unaffected by antibiotic medications.3 This makes it particularly useful in safeguarding your dog's gut health. Scientific studies support the efficacy of S. boulardii alongside antibiotic treatment, particularly in mitigating the risk of antibiotic-associated diarrhea - a common side effect that can cause distress for both pets and their owners.4 S. boulardii has also been shown to help stabilise the gut flora and reduce the frequency and severity of gastrointestinal disturbances in dogs with chronic gut issues such as Inflammatory Bowel Disease.5

Do … Nourish the body

A well-balanced, species-appropriate diet plays a pivotal role in not just your dog's overall health, but particularly in supporting the gut microbiome during and after antibiotic treatment. A diet rich in high-quality proteins, healthy fats, as well as fresh fruits and vegetables serves a dual purpose: it provides the essential energy your dog needs to fight off infection, while also offering the vital nutrients that beneficial gut bacteria rely on for their growth and maintenance. Importantly, a balanced, natural diet is free from artificial additives and preservatives, which can be detrimental to the gut flora. Therefore, focusing on high-quality, biologically appropriate foods is one of the most effective ways to support your dog's gastrointestinal health, particularly during the stress of illness and antibiotic therapy. This symbiotic relationship between diet and gut health is backed by a growing body of scientific evidence, which confirms that the composition of the microbiota is strongly influenced by what your dog eats, subsequently affecting their gastrointestinal health.6-8

Don’t … stop treatment prematurely

Some bacteria responsible for infections have built-in defence mechanisms that allow them to withstand the initial rounds of antibiotic treatment.9 While these mechanisms can fend off early doses, they do have their limits. Abruptly discontinuing antibiotic therapy before completing the full course can encourage the survival of these hardier bacteria, making them even more resistant to future antibiotic treatments. This creates a risk not only to your own pet but also to other animals they may come into contact with. Therefore, it's imperative to adhere to the entire antibiotic regimen as prescribed by your veterinarian.

Do’s and Don’ts - After antibiotic treatment

Do … Supplement with prebiotics and probiotics

One of the most effective ways to expedite your dog's gut health recovery following a course of antibiotics is the introduction of prebiotics into their diet. Unlike probiotics, which are live beneficial bacteria, prebiotics serve as nourishment for these good bacteria, helping them flourish and thereby restore a balanced gut microbiome. For example, marshmallow root and slippery elm are natural prebiotics that not only feed the beneficial bacteria, but which also has soothing properties for the digestive tract.10 Similarly, flaxseed meal is another excellent prebiotic option, rich in both fibre and omega-3 fatty acids, which aid in the support and growth of healthy gut bacteria.11 By incorporating prebiotics into your dog’s diet, you’re laying down the groundwork for a more robust microbial environment in your dog's gut. This facilitates quicker recovery from antibiotic-associated imbalances, boosts immune function, and aids in optimal nutrient absorption, setting your dog on a faster track to full health.

The administration of a high-quality probiotic supplement can also play an important role in the rapid recovery of your dog's gut microbiome following a course of antibiotics. Studies have highlighted the effectiveness of specific probiotic strains in rectifying microbial imbalance and promoting gut health.12, 13 For example, Enterococcus faecium is well-documented for its ability to boost immune function and outcompete harmful bacteria.14 Lactobacillus acidophilus aids in the production of lactic acid, creating an environment less hospitable for pathogenic bacteria.15 Similarly, strains of Bifidobacteria are known for their roles in enhancing nutrient absorption and modulating immune responses.16, 17  By supplementing with a multi strain probiotic, you're optimising the conditions for a swift and comprehensive recovery of your dog's gut microbiome post-antibiotic treatment.

Do … Provide additional digestive support

One aspect of antibiotic treatment that we often don’t consider is that antibiotics can significantly disrupt your dog's digestive capacity and nutrient absorption.18 The gut microbiome plays a pivotal role in breaking down complex carbohydrates, synthesising certain vitamins, and facilitating the uptake of minerals. Antibiotics, being non-selective, eliminate both pathogenic and beneficial bacteria, thereby impairing these vital functions. This microbial imbalance can lead to a cascade of digestive issues such as malabsorption of nutrients, reduced enzymatic activity, and compromised intestinal barrier function, commonly resulting in symptoms like diarrhoea, gas, and bloating. To help overcome this issue, supplementing your dog with digestive enzymes can be highly beneficial. These enzymes can assist in breaking down food components like proteins, fats, and carbohydrates, thereby supporting digestive function and improving nutrient absorption that may have been compromised during antibiotic therapy. Herbs such as chamomile and fennel can also aid digestion and reduce gas and bloating.

In addition to digestive enzymes, adding superfoods can also help boost nutrient intake and support overall well-being following bouts of illness. For instance, marine algae and chlorella are both rich in minerals and antioxidants that can help counter nutrient deficiencies.19, 20 Bovine Colostrum is a rich source of macro- and micro-nutrients, immune modulators, growth factors and other bioactive compounds that work to promote a healthy gut and enhance normal immune function.21, 22 Fulvic acid, a natural compound found in soil, supports cellular metabolism and works to improve the gut flora, nutrient absorption, and heal adverse disorders related to the gut.23 Incorporating these superfoods into your dog's diet can serve as an easy nutritional strategy to compensate for the challenges posed by antibiotic treatment.

Don’t … feed highly processed foods

The link between a high-carbohydrate, highly processed diet and poor gut health is well-established in human research24, and increasingly, these insights are being applied to canine nutrition as well. Just like in humans, dogs fed a diet predominantly composed of high-carbohydrate, processed kibble are more susceptible to a myriad of health issues ranging from obesity and diabetes to compromised gut health.25, 26 Extruded kibble often goes through intense heat and pressure during its manufacturing process, which can denature the proteins and degrade nutrients.27 Furthermore, such foods are frequently laden with artificial preservatives, fillers, and colourings that offer little to no nutritional value.

Commercial kibbles and natural raw food diets also differ widely in their nutrient sources and ratios (particularly of proteins and carbohydrates), and these differences have been shown to significantly alter the abundance and diversity of the canine gut microbiota.28 For example, dogs fed a natural raw food diet were found to have a more diverse and abundant microbial composition and more positive changes in markers of healthy gut function, than those fed a standard commercial kibble.29-32 As such, feeding a species-appropriate, nutrient-rich diet would seem to be the sensible approach if we want our dogs to achieve optimal gastrointestinal health and all of the health benefits that come from that following antibiotic treatment.

Summing up

Safeguarding your dog's gut health during and after a course of antibiotics is a multi-faceted endeavour that requires a well-considered approach. Do supplement with probiotics, particularly Saccharomyces boulardii. Opt for a species-appropriate diet, rich in natural nutrients, to promote gut biodiversity and overall health. Additionally, bolster your dog's nutrient intake with targeted supplements like prebiotics, other probiotics, superfoods, and digestive enzymes. On the flip side, don't make the mistake of cutting the antibiotic treatment short, as this can breed antibiotic-resistant bacteria. Likewise, avoid feeding a highly processed, carbohydrate-rich diet, as it can exacerbate gut imbalances and pave the way for chronic diseases. Taking a thoughtful approach to your dog's nutrition can significantly mitigate the adverse impacts of antibiotics and pave the way for long-term health and well-being.

About the Author - Narelle Cooke, Canine Nutritionist.

Narelle is a clinical Naturopath, Nutritionist and Herbalist for both people and pets, and operates her wellness clinic ‘Natural Health and Nutrition’ in Dural, Sydney.

Being a lifelong dog-owner and currently meeting the demands of three French Bulldogs, two German Shepherds and a Burmese cat, Narelle is as passionate about the health and wellbeing of our pets as she is about their owners. And it was this strong desire to see her own pets live their longest and best lives that led her to hours of personal research and additional study in the area of natural animal health and nutrition.

·  Bachelor of Health Science(Naturopathy) (ACNT)
·  Bachelor of Agricultural Science (honours) (The University of Melbourne)
·  Advanced Diploma of Naturopathy (AIAS)
·  Advanced Diploma of Nutritional Medicine (AIAS)
·  Advanced Diploma of Western Herbal Medicine (AIAS)
·  Certificate III in Dog Behaviour and Training (NDTF)
·  Certificate in Natural Animal Nutrition (CIVT)
·  Certificate in Animal Health Sciences (CIVT)
·  Certificate in Animal Nutrition (HATO)

If you liked this article, sign up to our Big Dog Fam Mail to receive more great pet health and happiness advice.

If you liked this article, please share on Facebook.

1. Ramirez, J., Guarner, F., et al. (2020). Antibiotics as Major Disruptors of Gut Microbiota. Front Cell Infect Microbiol. 10: p. 572912. DOI: 10.3389/fcimb.2020.572912.
2. Anthony, W.E., Wang, B., et al. (2022). Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Rep. 39(2): p. 110649. DOI: 10.1016/j.celrep.2022.110649.
3. Pais, P., Almeida, V., et al. (2020). Saccharomyces boulardii: What Makes It Tick as Successful Probiotic? J Fungi (Basel). 6(2). DOI: 10.3390/jof6020078.
4. Aktas, M.S., Borku, M.K., and O’zkanlar, Y.D., K. (2007). Efficacy of Saccharomyces boulardii as a probiotic in dogs with lincomycin induced diarrhoea. Bull Vet Inst Pulawy. 51: p. 365-369.
5. D'Angelo, S., Fracassi, F., et al. (2018). Effect of Saccharomyces boulardii in dog with chronic enteropathies: double-blinded, placebo-controlled study. Veterinary Record. 182(9): p. 258. DOI: 10.1136/vr.104241.
6. Garrigues, Q., Apper, E., et al. (2022). Gut microbiota development in the growing dog: A dynamic process influenced by maternal, environmental and host factors. Front Vet Sci. 9: p. 964649. DOI: 10.3389/fvets.2022.964649.
7. Hernandez, J., Rhimi, S., et al. (2022). Domestic Environment and Gut Microbiota: Lessons from Pet Dogs. Microorganisms. 10(5). DOI: 10.3390/microorganisms10050949.
8. Sinkko, H., Lehtimaki, J., et al. (2023). Distinct healthy and atopic canine gut microbiota is influenced by diet and antibiotics. R Soc Open Sci. 10(4): p. 221104. DOI: 10.1098/rsos.221104.
9. Zhou, G., Shi, Q.S., et al. (2015). The Three Bacterial Lines of Defense against Antimicrobial Agents. Int J Mol Sci. 16(9): p. 21711-21733. DOI: 10.3390/ijms160921711.
10. Morton, J.F. (1990). Mucilaginous plants and their uses in medicine. Journal of Ethnopharmacology. 29(3): p. 245-266.
11. Mueed, A., Shibli, S., et al. (2022). Flaxseed Bioactive Compounds: Chemical Composition, Functional Properties, Food Applications and Health Benefits-Related Gut Microbes. Foods. 11(20). DOI: 10.3390/foods11203307.
12. Xu, H., Zhao, F., et al. (2019). Metagenomic analysis revealed beneficial effects of probiotics in improving the composition and function of the gut microbiota in dogs with diarrhoea. Food Funct. 10(5): p. 2618-2629. DOI: doi: 10.1039/c9fo00087a.
13. Sivamaruthi, B.S., Kesika, P., and Chaiyasut, C. (2021). Influence of Probiotic Supplementation on Health Status of the Dogs: A Review. Applied Sciences. 11(23). DOI: 10.3390/app112311384.
14. Kim, B., Wang, Y.C., et al. (2019). Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. Elife. 8. DOI: 10.7554/eLife.45343.
15. Gao, H., Li, X., et al. (2022). The Functional Roles of Lactobacillus acidophilus in Different Physiological and Pathological Processes. J Microbiol Biotechnol. 32(10): p. 1226-1233. DOI: 10.4014/jmb.2205.05041.
16. Alessandri, G., Ossiprandi, M.C., et al. (2019). Bifidobacterial Dialogue With Its Human Host and Consequent Modulation of the Immune System. Front Immunol. 10: p. 2348. DOI: 10.3389/fimmu.2019.02348.
17. Barkhidarian, B., Roldos, L., et al. (2021). Probiotic Supplementation and Micronutrient Status in Healthy Subjects: A Systematic Review of Clinical Trials. Nutrients. 13(9). DOI: 10.3390/nu13093001.
18. Shobha (2019). Antibiotics and Nutritional Implications- The Drugs-Nutrients Interactions. Acta Scientific Nutritional Health. 3.6: p. 51-54.
19. Bito, T., Okumura, E., et al. (2020). Potential of Chlorella as a Dietary Supplement to Promote Human Health. Nutrients. 12(9). DOI: 10.3390/nu12092524.
20. Cotas, J., Leandro, A., et al. (2020). A Comprehensive Review of the Nutraceutical and Therapeutic Applications of Red Seaweeds (Rhodophyta). Life (Basel). 10(3). DOI: 10.3390/life10030019.
21. Playford, R.J. and Weiser, M.J. (2021). Bovine Colostrum: Its Constituents and Uses. Nutrients. 13(1). DOI: 10.3390/nu13010265.
22. Satyaraj, E., Reynolds, A., et al. (2013). Supplementation of diets with bovine colostrum influences immune function in dogs. Br J Nutr. 110(12): p. 2216-2221.
23. Winkler, J. and Ghosh, S. (2018). Therapeutic Potential of Fulvic Acid in Chronic Inflammatory Diseases and Diabetes. J Diabetes Res. 2018: p. 5391014. DOI: 10.1155/2018/5391014.
24. Seo, Y.S., Lee, H.B., et al. (2020). Dietary Carbohydrate Constituents Related to Gut Dysbiosis and Health. Microorganisms. 8(3). DOI: 10.3390/microorganisms8030427.
25. Orsolya Julianna, T., Kata, V., et al. (2020). Factors Affecting Canine Obesity Seem to Be Independent of the Economic Status of the Country-A Survey on Hungarian Companion Dogs. Animals (Basel). 10(8). DOI: 10.3390/ani10081267.
26. Hiney, K., Sypniewski, L., et al. (2021). Clinical health markers in dogs fed raw meat-based or commercial extruded kibble diets. Journal of Animal Science. 99(6). DOI: 10.1093/jas/skab133.
27. Tran, Q.D., Hendriks, W.H., and van der Poel, A.F.B. (2008). Effects of extrusion processing on nutrients in dry pet food. Journal of the Science of Food and Agriculture. 88(9): p. 1487-1493. DOI: 10.1002/jsfa.3247.
28. Huang, Z., Pan, Z., et al. (2020). The canine gastrointestinal microbiota: early studies and research frontiers. Gut Microbes. 11(4): p. 635-654. DOI: 10.1080/19490976.2019.1704142.
29. Kim, J., An, J.U., et al. (2017). Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform. Gut Pathog. 9: p. 68. DOI: 10.1186/s13099-017-0218-5.
30. Schmidt, M., Unterer, S., et al. (2018). The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets. PLoS One. 13(8): p. e0201279. DOI: 10.1371/journal.pone.0201279.
31. Bermingham, E.N., Maclean, P., et al. (2017). Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs. PeerJ. 5: p. e3019. DOI: 10.7717/peerj.3019.
32. Sandri, M., Dal Monego, S., et al. (2017). Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs. BMC Vet Res. 13(1): p. 65. DOI: 10.1186/s12917-017-0981-z.