Antibiotics and gut health

Recent veterinary studies have found that even short courses of antibiotics can have a lasting disruptive effect on the balance of the gut microbiome. Antibiotics save lives: no responsible dog owner would question their importance when an infection is present. But life-saving as they are, their use fuels the rise of multidrug-resistant strains – and can also leave lasting scars on the gut microbiome.

It’s easy to think of multidrug resistance (MDR) as the only danger from antibiotic use. But when harsh antibiotics disrupt the microbial community, the balance between helpful and harmful species can shift dramatically and destroy microbial harmony. Bacteria aren’t solitary operators: they communicate, coordinate and sometimes even cooperate inside the gut – a process known as quorum sensing. This complex yet delicate balance helps keep our dogs healthy.

Disruptors

Antibiotics don’t just silence harmful bacteria; they can disrupt the entire conversation in the gut, tipping the scales away from balance. Bacteria adapt quickly: when beneficial microbial populations are wiped out, other species move into the space. Microbial diversity is significantly reduced, leaving a microbiome that is more fragile – and potentially harbouring antibiotic-resistant species that make it more resilient to future treatment.

Science has shown the effects of antibiotics[1]: a less resilient gut, disrupting immune regulation. Even short courses of antibiotics can disrupt the gut equilibrium in dogs for weeks or even months afterwards; in one trial, dogs given routine antibiotics after surgery still showed significantly reduced microbial diversity up to three months later[2].Antibiotics can also wipe out the bacterial populations responsible for synthesis of vitamins, leading to potential deficiencies or reduced circulating levels, thus directly impacting the dog’s nutritional status and bioavailability.

Other research[3] found that the gut microbiome may not fully return to baseline after antibiotics, even with synbiotic supplementation[4]. Any dysbiosis[5] can:

  • weaken immune responses,
  • reduce microbial synthesis of crucial vitamins like Vitamins B and K, essential for coagulation,
  • impair the absorption of essential nutrients and
  • increase susceptibility to further illness.

The impact may be even greater in young or vulnerable dogs.

Reducing use

Scientists are now investigating new antimicrobial strategies and looking into limiting antibiotic use for certain illnesses, for example in the treatment of gastrointestinal inflammation, acute diarrhoea[6], pyoderma[7] and chronic enteropathy[8]. One study[9] found that “for canine non-infectious acute colitis, dietary management with an easily digestible diet (…) proved a superior management strategy compared to metronidazole. The omission of metronidazole reduced the adverse impact significantly on intestinal microbiota”. Comparisons have shown that nutraceuticals can be considered a better option than antibiotics[10].

One promising approach is quorum sensing interference[11] or inhibition, in other words blocking the chemical “chatter” used by bacteria to coordinate attacks. Instead of wiping out whole microbial populations (and damaging the gut in the process), quorum sensing inhibitors aim to silence the signals that trigger virulence and biofilm formation. However, while quorum sensing offers hope for the future, it’s still in its infancy.

Until such targeted approaches reach everyday veterinary practice, we can help to strengthen our dogs’ natural defences through nutrition – the one intervention already proven to help the gut recover and rebuild its balance.

Recovery: Practical strategies

Nutritional support may be especially important after longer or repeated antibiotic courses, when the microbiome is less able to bounce back on its own. Where the gut is weakened, whatever the cause, a diet that includes fibre, prebiotics and probiotics can make a measurable difference to recovery[12]. Veterinary options include targeted use of prebiotics, probiotics and synbiotics – combinations shown to support beneficial bacteria and enhance recovery of gut microbial diversity after antibiotic use[13].

Support from the kitchen

While we can’t replicate the clinical-grade probiotics and prebiotics used in research, everyday foods shouldn’t be downplayed. They can play an important role in sustaining microbial health. Variety is key: a diverse, plant-inclusive diet provides the broad chemistry that sustains microbial stability before, during and after antibiotic use. Fibre-rich vegetables help feed beneficial microbes and fuel the production of short-chain fatty acids that strengthen the gut barrier and regulate immune response.

After all, a healthy gut is likely to be more resilient and recover more quickly:

  1. Microbiome resilience is linked to a healthy, diverse baseline community: balanced, diverse microbiota support resilience and immune stability[14].
  2. Presence of beneficial taxa relates to stronger gut barrier and immune function: specific beneficial microbes linked to intestinal integrity and reduced inflammation[15].
  3. Dysbiosis slows recovery and increases instability: dogs with disrupted microbiomes take longer to return to balance after treatment[16].

As one study[17] put it: “… it may be that ‘resistance‘ or ‘susceptibility‘ to chronic infections to a certain extent is influenced by the diet and in particular by certain food components.”

A thriving gut microbiome

A healthy gut thrives on variety. Different foods feed different microbial communities, and the more diverse that community, the stronger the gut’s resilience. High-quality animal proteins and collagen-rich meats provide amino acids that help repair and maintain the gut lining while supporting the metabolism of beneficial microbes. Fibre is another key part of that equation: root vegetables such as celeriac, swede and carrots supply fermentable fibres and plant pigments that nourish bacteria producing short-chain fatty acids – essential for gut barrier integrity and immune balance. Leafy greens provide additional fibre, antioxidants and essential minerals, supporting detoxification processes and helping regulate inflammation within the gut environment.

Legumes and pseudo-grains contribute both fibre and resistant starch, supporting microbial fermentation and stable energy release. Seeds, especially chia and flax, offer soluble fibre and mucilage that aid digestion while providing minerals and omega fatty acids to maintain cellular health. Mushrooms, particularly shiitake and oyster, contain beta-glucans and other polysaccharides known to encourage beneficial bacteria and strengthen immune responses. Even herbs and aromatic plants – fennel, dill, parsley – add mild antimicrobial and antioxidant activity that helps maintain microbial harmony without the collateral damage of stronger agents. The more these foods appear, in rotation and combination, the more adaptable and self-regulating the gut becomes.

Nutrition matters because it can help to create resilience before treatment and restore balance after illness or antibiotic use – and to prevent longer-term consequences. Supporting the microbiome with fibre, synbiotics and nutraceuticals doesn’t just aid recovery; it helps ensure that beneficial bacteria can compete with – and contain – their more troublesome counterparts.

And support your dog.

****

References:

[1] Stavroulaki EM, Suchodolski JS, Xenoulis PG. Effects of antimicrobials on the gastrointestinal microbiota of dogs and cats. Vet J. 2023 Jan;291:105929. doi: 10.1016/j.tvjl.2022.105929. Epub 2022 Nov 24. PMID: 36427604.
[2] Collier AJ, Gomez DE, MacIver MA, Verbrugghe A, Weese JS, Blois SL. Assessing changes to the fecal microbiota in dogs undergoing elective orthopedic surgery: A preliminary investigation. PLoS One. 2025 Jun 2;20(6):e0325163. doi: 10.1371/journal.pone.0325163. PMID: 40455707; PMCID: PMC12129194.
[3] Pilla R, Gaschen FP, Barr JW, Olson E, Honneffer J, Guard BC, Blake AB, Villanueva D, Khattab MR, AlShawaqfeh MK, Lidbury JA, Steiner JM, Suchodolski JS. Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. J Vet Intern Med. 2020 Sep;34(5):1853-1866. doi: 10.1111/jvim.15871. Epub 2020 Aug 28. PMID: 32856349; PMCID: PMC7517498.
[4] Marshall-Jones ZV, Patel KV, Castillo-Fernandez J, Lonsdale ZN, Haydock R, Staunton R, Amos GCA, Watson P. Conserved signatures of the canine faecal microbiome are associated with metronidazole treatment and recovery. Sci Rep. 2024 Mar 4;14(1):5277. doi: 10.1038/s41598-024-51338-7. PMID: 38438389; PMCID: PMC10912219.
[5] Deschamps C, Apper E, Brun M, Durif C, Denis S, Humbert D, Blanquet-Diot S. Development of a new antibiotic-induced dysbiosis model of the canine colonic microbiota. Int J Antimicrob Agents. 2024 Apr;63(4):107102. doi: 10.1016/j.ijantimicag.2024.107102. Epub 2024 Feb 5. PMID: 38325721.
[6] Shmalberg J, Montalbano C, Morelli G, Buckley GJ. A Randomized Double Blinded Placebo-Controlled Clinical Trial of a Probiotic or Metronidazole for Acute Canine Diarrhea. Front Vet Sci. 2019 Jun 4;6:163. doi: 10.3389/fvets.2019.00163. PMID: 31275948; PMCID: PMC6593266.
[7] Valentine B. Treating pyoderma without the use of systemic antibiotics. Can Vet J. 2019 Dec;60(12):1361-1363. PMID: 31814647; PMCID: PMC6855222.
[8] Kathrani A. Dietary and Nutritional Approaches to the Management of Chronic Enteropathy in Dogs and Cats. Vet Clin North Am Small Anim Pract. 2021 Jan;51(1):123-136. doi: 10.1016/j.cvsm.2020.09.005. Epub 2020 Oct 29. PMID: 33131914.
[9] Rudinsky, A. J., Parker, V. J., Winston, J., Cooper, E., Mathie, T., Howard, J. P., Bremer, C. A., Yaxley, P., Marsh, A., Laxalde, J., Suchodolski, J., & Perea, S. (2022). Randomized controlled trial demonstrates nutritional management is superior to metronidazole for treatment of acute colitis in dogs. Journal of the American Veterinary Medical Association, 260(S3), S23-S32. Retrieved Nov 1, 2025, from https://doi.org/10.2460/javma.22.08.0349
[10] Pignataro, Giulia & Prinzio, Roberta & Crisi, Paolo & Bela, Benedetta & Fusaro, Isa & Trevisan, Carlo & Acetis, Luigi & Gramenzi, Alessandro. (2021). Comparison of the Therapeutic Effect of Treatment with Antibiotics or Nutraceuticals on Clinical Activity and the Fecal Microbiome of Dogs with Acute Diarrhea. Animals. 11. 1484. 10.3390/ani11061484.
[11] Lima EMF, Winans SC, Pinto UM. Quorum sensing interference by phenolic compounds – A matter of bacterial misunderstanding. Heliyon. 2023 Jun 26;9(7):e17657. doi: 10.1016/j.heliyon.2023.e17657. PMID: 37449109; PMCID: PMC10336516.
[12] Tolbert MK, Murphy M, Gaylord L, Witzel-Rollins A. Dietary management of chronic enteropathy in dogs. J Small Anim Pract. 2022 Jun;63(6):425-434. doi: 10.1111/jsap.13471. Epub 2022 Jan 6. PMID: 34991182.
[13] Sung-Jae Kim, Hee-Chun Chung, Soo-Yeon Park, Jae-Myun Lee, Jeong-Hee Han, Beneficial effects of probiotics on dysbiosis of gut microbiota induced by antibiotic treatment in healthy dogs, Research in Veterinary Science, Volume 191, 2025, 105674, ISSN 0034-5288, https://doi.org/10.1016/j.rvsc.2025.105674.
[14] Pilla R, Suchodolski JS. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. Front Vet Sci. 2020 Jan 14;6:498. doi: 10.3389/fvets.2019.00498. PMID: 31993446; PMCID: PMC6971114.
[15] Tolbert MK, Murphy M, Gaylord L, Witzel-Rollins A. Dietary management of chronic enteropathy in dogs. J Small Anim Pract. 2022 Jun;63(6):425-434. doi: 10.1111/jsap.13471. Epub 2022 Jan 6. PMID: 34991182.
[16] Pilla R, Gaschen FP, Barr JW, Olson E, Honneffer J, Guard BC, Blake AB, Villanueva D, Khattab MR, AlShawaqfeh MK, Lidbury JA, Steiner JM, Suchodolski JS. Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. J Vet Intern Med. 2020 Sep;34(5):1853-1866. doi: 10.1111/jvim.15871. Epub 2020 Aug 28. PMID: 32856349; PMCID: PMC7517498.
[17] Givskov M. Beyond nutrition: health-promoting foods by quorum-sensing inhibition. Future Microbiol. 2012 Sep;7(9):1025-8. doi: 10.2217/fmb.12.84. PMID: 22953702.

 

Important Considerations:

  • Always consult your veterinarian before making any significant dietary changes, particularly where there are pre-existing health conditions or dietary restrictions.
  • If you are feeding commercial food, check the label for ingredients before giving more. Excessive intake of any foods can have adverse effects.
  • Ensure (where possible) that you use high-quality, organic products specifically formulated for pets (or better still, human grade ingredients) to avoid any potential adverse effects.
  • Introduce new foods gradually to avoid adverse effects such as gastrointestinal upset or diarrhoea.
  • I provide nutritional information purely as a helpful guide. Nutritional information on ingredients is obtained from the US Department of Agriculture’s FoodData Central site (https://fdc.nal.usda.gov/index.html) and any nutritional information provided in recipes is based on an online calculator: calories and other information will vary based on brands, ingredients and other factors.
  • Check nutrient levels and recommendations for your dog’s weight, age and activity. For example this nutritional guideline produced by FEDIAF.
  • I am not a professional canine nutritionist but supporting research is cited.
  • The recipes shared were created by me and tested in my kitchen – and tasted and approved by our doggy friends!