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Exploring the Impact of Diet on Gut Microbiome Diversity and Resilience Following Antibiotic Exposure

At BIOME9, we’re passionate about supporting the next generation of scientists, from providing hands-on laboratory experience to making our data available for meaningful student research.

Beth, an undergraduate student at University Centre Reaseheath, used anonymised BIOME9 microbiome data to investigate the relationship between the canine gut microbiome, health and nutrition as part of her dissertation — research that earned her a First.

Here, Beth shares the science behind her project, what her research revealed, and what her findings could tell us about the complex world of the canine gut microbiome.

September 18, 2026 • 7 min read

Beth McCarthy BSc

Student Researcher

As a Canine Clinical Behaviour student at University Centre Reaseheath, I have developed a particular interest in canine nutrition and microbiome science. Wanting to explore this field further, I chose to focus my dissertation on how diet may influence gut microbiome diversity and resilience following antibiotic exposure in healthy adult dogs.

Through the valuable opportunity to work with anonymised data provided by BIOME9, I
investigated a relatively underexplored area of canine microbiome research. This project
allowed me to combine my interests in nutrition and gut health while gaining experience
analysing real-world data and interpreting findings within existing research. This interest developed during my studies as I became increasingly aware of the impact of nutrition on canine health and behaviour, and I wanted to better understand how diet may support recovery following antibiotic treatment.

The canine gut microbiome is increasingly recognised as a cornerstone of health, influencing digestion, immune function, metabolism and even behaviour through the gut-brain axis (1,2). Like any ecosystem, it is constantly responding to change. Diet, environment, age, stress and medication can all shape the microbial communities living within the gastrointestinal tract (1). Among these, antibiotics are known to have one of the most profound effects, often reducing microbial diversity and disrupting the balance of beneficial bacteria (3–7). This is particularly relevant in the United Kingdom, where an estimated 53% of dogs are prescribed antibiotics during their lifetime, highlighting the widespread potential for antibiotic-associated microbiome disruption (8).

While antibiotics remain an essential tool in veterinary medicine, less attention has been
given to microbiome resilience - the ability of the microbial community to recover following disturbance and return to a stable, functional state (9–11). Although previous studies have explored how diet influences the canine microbiome under normal conditions, far less is known about whether diet plays a role in recovery following antibiotic exposure, leaving an important gap in current understanding.

What this study looked at:

To investigate this question, I analysed anonymised microbiome data from 268 healthy adult dogs after data cleaning provided by BIOME9. The study examined two key measures of microbiome health: microbial diversity (Shannon Diversity Index) and microbiome resilience (BIOME9 resilience score).

Based on the majority of previous studies reporting higher microbial diversity in raw-fed
dogs, it was hypothesised that raw-fed dogs would show greater diversity and resilience
following antibiotic exposure. However, the results told a more complex story. While
microbial diversity differed between groups, kibble-fed dogs with a history of antibiotics
showed significantly higher diversity than raw-fed dogs (Figure 1).

What the findings suggest:

When compared with existing literature, only a small number of studies report higher
microbial diversity in kibble-fed dogs. Notably, when these were examined more closely, they often involved diets with higher fermentable fibre content than the raw diets they were compared against (15, 17). Fibre is widely recognised as a key fuel source for beneficial gut bacteria and may support recovery following disturbance (19, 20–24). This suggests that fibre content, rather than broad diet type, may help explain the patterns observed across studies.

In contrast, resilience showed no clear differences between dietary groups. Given that
resilience is influenced by many factors beyond diet - including age, environment, genetics, health status and previous medication exposure (9, 24) - this is perhaps not surprising. This is also an area that remains relatively underexplored in canine microbiome research, particularly in the context of antibiotic exposure (11).

Why this matters:

From both an industry and pet owner perspective, these findings are particularly relevant. Antibiotic-associated microbiome disruption is common in companion animals, yet evidence- based guidance on post-antibiotic nutrition remains limited (3, 5, 6, 8). The gut microbiome plays a central role in digestion, immune function and metabolic health (1), so disruption can have implications beyond the treatment period. Effective recovery is therefore important for supporting long-term health outcomes and potentially reducing the need for future interventions.

While further research is needed to better understand what drives resilience and recovery after antibiotic exposure, this study highlights that diet-related differences in microbial diversity are present following antibiotic exposure, suggesting diet plays a bigger role in gut health than we often realise. This may help improve how post-antibiotic nutritional strategies are interpreted and applied in practice to aid recovery.

References:

1. Kim, H., Chae, Y., Cho, J. H., Song, M., Kwak, J., Doo, H., Choi, Y., Kang, J., Yang, H.,Lee, S., Keum, G. B., Wattanaphansak, S., Kim, S., & Kim, H. B. (2025). Understanding the diversity and roles of the canine gut microbiome. Journal of Animal Science and Biotechnology, 16(1), 95. https://doi.org/10.1186/s40104-025-01235-4
2. Crisante, A., Newberry, F., Clegg, S. R., Mitchell, G. L., Pike, T. W., Ratcliffe, V., Spain, A., Wilkinson, A., Zulch, H., & Mills, D. S. (2025). A critical review of research concerning the gut microbiome in dogs and its relationship with behaviour. Applied Animal Behaviour Science, 292, 106755. https://doi.org/10.1016/j.applanim.2025.106755
3. Marshall-Jones, Z. V., Patel, K. V., Castillo-Fernandez, J., Lonsdale, Z. N., Haydock, R., Staunton, R., Amos, G. C. A., & Watson, P. (2024). Conserved signatures of the canine faecal microbiome are associated with metronidazole treatment and recovery. Scientific Reports, 14(1), 5277. https://doi.org/10.1038/s41598-024-513387
4. Mondo, E., De Cesare, A., Manfreda, G., Sala, C., Cascio, G., Accorsi, P. A., Marliani, G., & Cocchi, M. (2020). Depression and Microbiome—Study on the Relation and Contiguity between Dogs and Humans. Applied Sciences, 10(2), 573. https://doi.org/10.3390/app10020573
5. Pilla, R., & Suchodolski, J. S. (2020). The role of the canine gut microbiome and metabolome in health and gastrointestinal disease. Frontiers in Veterinary Science, 6, 502799. https://doi.org/10.3389/fvets.2019.00498
6. Whittemore, J. C., Price, J. M., Moyers, T., & Suchodolski, J. S. (2021). Effects of synbiotics on the fecal microbiome and metabolomic profiles of healthy research dogs administered antibiotics: a randomized, controlled trial. Frontiers in Veterinary Science, 8, 665713. https://doi.org/10.3389/fvets.2021.665713
7. Connelly, S., Fanelli, B., Hasan, N. A., Colwell, R. R., & Kaleko, M. (2019). Oral betalactamase protects the canine gut microbiome from oral amoxicillin-mediated damage. Microorganisms, 7(5), 150. https://doi.org/10.3390/microorganisms7050150
8. Del Solar Bravo, R. E., Sharman, M. J., Raj, J., & Scudder, C. (2023). Antibiotic therapy in dogs and cats in general practice in the United Kingdom before referral. Journal of Small Animal Practice, 64(8), 499–506. https://doi.org/10.1111/jsap.13615
9. Dogra, S. K., Doré, J., & Damak, S. (2020). Gut microbiota resilience: Definition, link to health and strategies for intervention. Frontiers in Microbiology, 11, 572921. https://doi.org/10.3389/fmicb.2020.572921
10. Philippot, L., Griffiths, B. S., & Langenheder, S. (2021). Microbial community resilience across ecosystems and multiple disturbances. Microbiology and Molecular Biology Reviews, 85(2). https://doi.org/10.1128/mmbr.00026-20
11. Sommer, F., Anderson, J. M., Bharti, R., Raes, J., & Rosenstiel, P. (2017). The resilience of the intestinal microbiota influences health and disease. Nature Reviews Microbiology, 15(10), 630–638. https://doi.org/10.1038/nrmicro.2017.58
12. Safarchi, A., Al-Qadami, G., Tran, C. D., & Conlon, M. (2025). Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges. Frontiers in Microbiology, 16, 1559521. https://doi.org/10.3389/fmicb.2025.1559521
13. Castañeda, S., Ariza, G., Rincón-Riveros, A., Muñoz, M., & Ramírez, J. D. (2023). Diet- induced changes in fecal microbiota composition and diversity in dogs (Canis lupus familiaris): A comparative study of BARF-type and commercial diets. Comparative Immunology Microbiology and Infectious Diseases, 98, 102007. https://doi.org/10.1016/j.cimid.2023.102007

14. Kim, J., An, J. U., Kim, W., Lee, S., & Cho, S. (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 Pathogens, 9(1), 68. https://doi.org/10.1186/s13099017- 0218-5
15. Hiney, K., Sypniewski, L., DeSilva, U., Pezeshki, A., Rudra, P., Goodarzi, P., Willis, E., & McFarlane, D. (2024). Fecal microbiota composition, serum metabolomics, and markers of inflammation in dogs fed a raw meat-based diet compared to those on a kibble diet. Frontiers in Veterinary Science, 11,
1328513. https://doi.org/10.3389/fvets.2024.1328513
16. Rojas, C. A., Park, B., Scarsella, E., Jospin, G., Entrolezo, Z., Jarett, J. K., Martin, A., & Ganz, H. H. (2024). Species-level characterization of the core microbiome in healthy dogs using full-length 16S rRNA gene sequencing. Frontiers in Veterinary Science, 11, 1405470. https://doi.org/10.3389/fvets.2024.1405470
17. Alessandri, G., Milani, C., Mancabelli, L., Mangifesta, M., Lugli, G. A., Viappiani, A., Duranti, S., Turroni, F., Ossiprandi, M. C., Van Sinderen, D., & Ventura, M. (2019). Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. Environmental Microbiology, 21(4), 1331–1343. https://doi.org/10.1111/1462-2920.14540
18. Xu, J., Becker, A. A. M. J., Luo, Y., Zhang, W., Ge, B., Leng, C., Wang, G., Ding, L., Wang, J., Fu, X., & Janssens, G. P. J. (2021). The fecal microbiota of dogs switching to a raw diet only partially converges to that of wolves. Frontiers in Microbiology, 12, 701439. https://doi.org/10.3389/fmicb.2021.701439
19. Cronin, P., Joyce, S. A., O’Toole, P. W., & O’Connor, E. M. (2021). Dietary fibre modulates the gut microbiota. Nutrients, 13(5), 1655. https://doi.org/10.3390/nu13051655
20. Menni, C., Jackson, M. A., Pallister, T., Steves, C. J., Spector, T. D., & Valdes, A. M. (2017). Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain. International Journal of Obesity, 41(7),
1099–1105. https://doi.org/10.1038/ijo.2017.66
21. Moura, I. B., & Buckley, A. M. (2024). Using nutrition to help recovery from infections. Current Opinion in Gastroenterology, 41(1), 54–58. https://doi.org/10.1097/mog.0000000000001068
22. Tanes, C., Bittinger, K., Gao, Y., Friedman, E. S., Nessel, L., Paladhi, U. R., Chau, L., Panfen, E., Fischbach, M. A., Braun, J., Xavier, R. J., Clish, C. B., Li, H., Bushman, F. D., Lewis, J. D., & Wu, G. D. (2021). Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host & Microbe, 29(3), 394–407.e5. https://doi.org/10.1016/j.chom.2020.12.012
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100070. https://doi.org/10.1016/j.medmic.2022.100070
24. Crisante, A., Newberry, F., Clegg, S. R., Mitchell, G. L., Pike, T. W., Ratcliffe, V., Spain, A., Wilkinson, A., Zulch, H., & Mills, D. S. (2025). A critical review of research concerning the gut microbiome in dogs and its relationship with behaviour. Applied Animal Behaviour Science, 292, 106755. https://doi.org/10.1016/j.applanim.2025.106755

Frequently asked questions

The microbiome is the name given to the collection of microbes, mostly bacteria, but also fungi and protozoa, that exist within your dog’s gut. It is a diverse and complex microbial community which can directly affect health and wellbeing. We know that 90% of a human’s body cells are microbes, with only 10% being human cells – it’s just that human cells are markedly larger than the microbes. It’s similar for our four-legged friends. Testing the microbiome gives us an idea of exactly which bacteria are present in your dog’s gut and this can help indicate existing or future health problems.
A healthy diversity within the microbiome has been found to be an accurate indicator of overall health and wellbeing. If your dog appears healthy, but has an imbalance in their microbiome, then this could be an indicator of a potential future health issue. If your dog has any existing health complaints, then improving the health of their microbiome can help to improve immune system health and overall wellbeing, as well as improving disease symptoms.
Testing and treatment have the potential to help with a whole range of different health complaints. The immune system is very closely associated with the gut, so any imbalance in the microbiome can influence immune system health, overall vitality and wellbeing. Our supplement recommendations are also tailored to your individual dog, with specific ranges designed to help with gastrointestinal inflammation, joint problems, allergies and skin complaints, to name a few.
All you need to do is order a kit online and fill in our questionnaire about your dog and their general health. We will then send the kit out to you by post. You then just need to collect a sample and return it to us, again by post. Once the test is performed, we will email the results directly to you.
You do not need to get your vet’s permission to test, or talk to them about performing the test beforehand. We do recommend that you pass on a copy of your test results to your regular vets, as it may help them in understanding your pet’s current health, and any future complaints they may have.