The gut microbiome in companion animal nutrition: emerging science, functional diets, and personalized pet food strategies

The gut microbiome has emerged as a central determinant of health, metabolism, immune competence, and disease outcomes in companion animals, playing a critical role in maintaining overall physiological balance. Advances in high-throughput sequencing technologies, metagenomics, and metabolomics have revealed highly diverse and complex microbial ecosystems in dogs and cats that interact dynamically with dietary inputs, host genetics, age, lifestyle, and environmental factors. These microbial communities influence nutrient digestion, bioavailability, short-chain fatty acid production, inflammatory pathways, and systemic metabolic regulation.

This review synthesizes current scientific evidence linking the gut microbiome to nutrient metabolism, immune modulation, gastrointestinal function, metabolic disorders, obesity, and functional dietary responses in pets. We discuss the mechanisms through which diet composition, ingredient quality, and feeding strategies shape microbial diversity, stability, and metabolic activity. In addition, we evaluate the role of emerging functional ingredients—including prebiotics, probiotics, postbiotics, synbiotics, and fermented components—in modulating gut health. Personalized nutrition strategies based on microbiome profiling are also explored. Finally, we identify research gaps and future directions for integrating microbiome science into innovative pet food formulation and clinical veterinary practice.

1. Suchodolski JS. Microbiome sequencing in companion animals: challenges and opportunities. Vet Clin North Am Small Anim Pract. 2020;50(2):325–339.

2. Mackie RI, et al. Ecology and significance of the canine and feline gut microbiome. J Anim Sci. 2015;93(12):5485–5498.

3. Kumar, R., Goswami, M., & Pathak, V. (2024). Gas Chromatography Based Analysis of fatty acid profiles in poultry byproduct-based pet foods: Implications for Nutritional Quality and Health Optimization. Asian Journal of Research in Biochemistry, 14(4), 1-17. https://doi.org/10.9734/ajrb/2024/v14i4289

4. Kumar, R., Goswami, M., Pathak, V., & Singh, A. (2024). Effect of binder inclusion on poultry slaughterhouse byproducts incorporated pet food characteristics and palatability. Animal Nutrition and Feed Technology, 24(1), 177-191. DOI: 10.5958/0974-181X.2024.00013.1

5. Kumar, R., Goswami, M., Pathak, V., Bharti, S.K., Verma, A.K., Rajkumar, V. and Patel, P. 2023. Utilization of poultry slaughter byproducts to develop cost effective dried pet food. Anim. Nutr. Technol., 23: 165-174. DOI: 10.5958/0974-181X.2023.00015.X

6. Hooda S, et al. Effects of dietary protein on canine gut microbiota: implications for health. J Nutr Sci. 2012;1:e35.

7. Kumar R, Goswami M, Pathak V. Innovations in pet nutrition: investigating diverse formulations and varieties of pet food: mini review. MOJ Food Process Technols. 2024;12(1):86‒89. DOI: 10.15406/mojfpt.2024.12.00302

8. Kumar R, Goswami M. Harnessing poultry slaughter waste for sustainable pet nutrition: a catalyst for growth in the pet food industry. J Dairy Vet Anim Res. 2024;13(1):31‒33. DOI: 10.15406/jdvar.2024. 13.00344

9. Kumar, R. (2024). Promoting Pet Food Sustainability: Integrating Slaughterhouse By-products and Fibrous Vegetables Waste. Acta Scientific Veterinary Sciences, 6, 07-11. http://dx.doi.org/10.31080/ASVS.2024.06.0871

10. Swanson KS, et al. Impact of dietary macronutrients on canine microbial ecology. Anim Feed Sci Technol. 2011;166–167:712–722.

11. Verbrugghe A, et al. Prebiotic fiber supplementation in dogs: effects on microbiota and fermentation. J Anim Physiol Anim Nutr. 2011; 95(5):628–637.

12. Panasevich MR, et al. Dietary polyphenols influence canine microbiome and metabolome. Front Vet Sci. 2019;6:123.

13. Weese JS, et al. Probiotic supplementation in dogs and cats: clinical efficacy and safety. Can Vet J. 2010;51(7):701–708.

14. Stahl B, et al. Postbiotics: definition and functional applications in companion animal nutrition. J Anim Sci Biotechnol. 2021;12:56.

15. Guard BC, et al. Effect of dietary carbohydrate and fiber on gastrointestinal microbiota of healthy dogs. J Anim Sci. 2015;93(6):S45–S46.

16. Kumar, R., & Goswami, M. (2024). Exploring Palatability in Pet Food: Assessment Methods and Influential Factors. International Journal of Livestock Research, 14(4).

17. Kumar, R., & Goswami, M. (2024). Feathered nutrition: unlocking the potential of poultry byproducts for healthier pet foods. Acta Scientific Veterinary Sciences. (ISSN: 2582-3183), 6(4).

18. Kumar, R., & Goswami, M. (2024). Optimizing Pet Food Formulations with Alternative Ingredients and Byproducts. Acta Scientific Veterinary Sciences (ISSN: 2582-3183), 6(4).

19. Kumar, R., & Sharma, A. (2024). A Comprehensive Analysis and Evaluation of Various Porcine Byproducts in Canine Diet Formulation. Asian Journal of Research in Animal and Veterinary Sciences, 7(3), 236-246. https://doi.org/10.9734/ajravs/2024/v7i3308

20. Middelbos IS, et al. Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing. PLoS ONE. 2010;5(3) :e9768.

21. Beloshapka AN, et al. Impact of plant protein concentrates on canine gut microbiota when compared to meat protein. Front Microbiol. 2013;4:193.

22. Bermingham EN, et al. The effect of dietary prebiotic supplementation with inulin in obese dogs. Br J Nutr. 2012;108(S1):S100–S103.

23. Zentek J, et al. Effects of diets supplemented with chicory on fecal microbiota and fermentative end products in dogs. J Anim Sci. 2003;81(8):2000–2009.

24. Kumar, R., & Sharma, A. (2024). Deciphering new nutritional substrates for precision pet food formulation. International Journal of Veterinary Sciences and Animal Husbandry.https://doi.org/10. 22271/veterinar y, 202(4), v9.

25. Kumar, R., & Sharma, A. (2024). Prebioticdriven Gut Microbiota Dynamics: Enhancing Canine Health via Pet Food Formulation. International Journal of Bio-resource and Stress Management, 15(Jun, 6), 01- 15. https://doi.org/10.23910/1.2024.5359

26. Kumar, R., & Sharma, A. (2024). Review of Pet Food Packaging in the US Market: Future Direction Towards Innovation and Sustainability. Annual Research & Review in Biology, 39(6), 16-30. https://doi.org/10.9734/arrb/2024/v39i62085

27. Kumar, R., Goswami, M. and Pathak, V. (2023). Enhancing Microbiota Analysis, Shelf-life, and Palatability Profile in Affordable Poultry Byproduct Pet Food Enriched with Diverse Fibers and Binders. J. Anim. Res., 13(05): 815-831. DOI: 10.30954/2277-940X.05.2023.24

28. Coelho LP, et al. Similarity of canine and human gut microbiomes in the context of obesity and weight loss. Microbiome. 2018;6:72.

29. Kim HJ, et al. Gut microbiota key functional features in dogs and cats with chronic enteropathy. Anim Microbiome. 2021;3(1):57.

30. Garcia‑Millán C, et al. Effects of probiotic yeast supplementation on feline gastrointestinal health. Vet Microbiol. 2021;255:109020.

31. Garcia‑Rodriguez A, et al. Dogs’ gut microbiota responses to dietary prebiotics: a randomized controlled trial. Front Vet Sci. 2022;9:825174.

32. Werner JA, et al. Gut microbiome alterations in cats with derived metabolic disease and the role of diet. Front Microbiol. 2021;12:712164.

33. Park S, et al. Effects of diet and antibiotics on the canine gut microbiome: implications for clinical nutrition. Nutrients. 2020;12(2):432.

34. Kumar, R., Goswami, M., Pathak, V., Verma, A.K. and Rajkumar, V. 2023. Quality improvement of poultry slaughterhouse byproducts-based pet food with incorporation of fiber-rich vegetable powder. Explor. Anim. Med. Res., 13(1): 54-61. DOI: 10.52635/eamr/13.1.54-61

35. Kumar, R., Thakur, A., & Sharma, A. (2023). Comparative prevalence assessment of subclinical mastitis in two crossbred dairy cow herds using the California mastitis test. J Dairy Vet Anim Res, 12(2), 98-102 http://dx.doi.org/10.15406/jdvar.2023.12.00331

36. Alexander J, et al. The role of butyrate and other microbial metabolites in immune modulation in pets. Vet Immunol Immunopathol. 2021;235:110206.

37. Dodd D, et al. Microbial contributions to systemic metabolism: insights from companion animal studies. Trends Microbiol. 2022;30(4):307–323.

38. Liu Y, et al. Personalized microbiome nutrition and feeding strategies in companion animals: present evidence and future perspectives. Front Nutr. 2023;10:1140722.

39. Heaney C, et al. Influence of diet and microbiota on inflammation and metabolic syndrome in dogs and cats. J Nutr Health Aging. 2021;25(5):526– 538.