The Microbiome

Defining the Gut Microbiome

The gut microbiome of cats and dogs have an estimated 100 trillion microorganisms including bacteria, fungi, protozoa, archaea, and viruses living in their gastrointestinal tracts and more specifically, the large intestine. Collectively making up the gut microbiome, microbes help complete normal physiological and digestive functions influencing the health of the host animal.

Symptoms Related to the Gut Microbiome

In a healthy gut, a balanced, healthy community includes a diverse community of microbes functioning commensally to maintain health. An imbalance of the gut microbiome can be caused by a variety of factors, including disease, age, diet, and medications—especially antibiotics.1–4 When a patient experiences an imbalance or dysbiosis, the altered functions are reflected in the pet’s health. For example, decreases in commensal microbes in the large intestine may increase the number of primary bile acids passed in the stool resulting in a pet with secretory diarrhea.

A diverse, balanced gut microbiome includes trillions of bacteria and other microbes. This dynamic community is crucial for the proper functioning of your patient’s metabolic, and physiological processes.

An imbalanced gut microbiome may contain only a few different bacterial groups. When key bacteria groups are missing, there will be changes in normal metabolic and physiological functions resulting in the development of a variety of clinical symptoms.

Effects of Antibiotics on the Gut Microbiome

While antibiotics are necessary for the treatment of systemic infections, veterinary professionals are now more strongly considering their antimicrobial stewardship when prescribing antibiotics for acute symptoms of illness in pets.5 Excessive prescription of antibiotics has also been linked to antimicrobial resistance in population-based studies.5,6

Our knowledge of the gut microbiome and how medications, including antibiotics, affect the overall diversity within the microbiome is growing exponentially by the day.7–9 Knowing the extent of elimination of the native gut bacteria caused by broad spectrum antibiotics allows veterinarians to make more educated decisions on therapy options that better align with antimicrobial stewardship principles.10 Even when antibiotics are a necessity for a patient, there are ways to support the gut bacterial community during and after treatment.11

Gaining Insights Into Your Patient’s Gut Microbiome

Microbiome testing is a great way to obtain a snapshot of your patient’s gut health. Being able to identify why your patient is experiencing symptoms can help direct your treatment options and provide better outcomes for your patients.

Find out what’s going on in your patient’s gut

How Diet Impacts Gut Health in Pets

Diet is an important way to manage your patient’s gut microbiome. What your patient eats determines, in part, which kinds of microbes thrive and multiply in their gut.

Feeding a complete and balanced diet is the best way to support the gut microbiome. Microbes that live in the gut digest the non-absorbed or indigestible portion of your patient’s food. Therefore, what is fed to a cat or dog will directly influence specific groups of gut microbes to thrive and multiply. For example, diets that contain a lot of carbohydrates encourage the growth of particular groups of gut microbes that prefer this nutrient. This encourages excessive multiplication that may crowd out other important microbial groups and reduce diversity in the microbiome. Having an excess of any microbial group can be as detrimental for health as having insufficient amounts, with balance in the microbiome creating the best outline to support health.

Manipulation of the macronutrients in a patient’s diet is one way we can influence the microbes in the GI tract. This includes the type and digestibility of the nutrients. Diets that have a lower digestibility will have a larger provision of nutrients reaching the GI microbes. The key nutritional factors must also be taken into consideration. Ensuring that nutrients meet any metabolic, disease state, or life stage requirements of the patient. More is not necessarily better; it is about meeting the nutritional requirements in sufficient amounts for both dogs and cats to improve and support health.

How Probiotics Affect Gut Health in Pets

Bacteria probiotic supplements should contain beneficial bacteria, though most studies on bacteria probiotics are focused on their effects on the gut microbiome of human’s or mice, not cats and dogs. While these products may temporarily improve some digestive symptoms, the microorganisms they contain are unable to correct an imbalance. In fact, new research suggests that probiotics can actually interfere with the recovery of the gut microbiome after antibiotic use.

Learn more about probiotics, prebiotics, and postbiotics


  1. Ramirez J, Guarner F, Bustos Fernandez L, Maruy A, Sdepanian VL, Cohen H. Antibiotics as Major Disruptors of Gut Microbiota. Front Cell Infect Microbiol. 2020;10:572912. 
  2. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-563. 
  3. Bosco N, Noti M. The aging gut microbiome and its impact on host immunity. Genes Immun. 2021;22(5-6):289-303. 
  4. Wiertsema SP, van Bergenhenegouwen J, Garssen J, Knippels LMJ. The Interplay between the Gut Microbiome and the Immune System in the Context of Infectious Diseases throughout Life and the Role of Nutrition in Optimizing Treatment Strategies. Nutrients. 2021;13(3). doi:10.3390/nu13030886
  5. Kim Y, Leung MHY, Kwok W, Fournié G, Li J, Lee PKH, et al. Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome. Animal Microbiome. 2020;2(1):1-14. 
  6. Yang Y, Hu X, Li W, Li L, Liao X, Xing S. Abundance, diversity and diffusion of antibiotic resistance genes in cat feces and dog feces. Environ Pollut. 2022;292(Pt A):118364. 
  7. Pilla R, Gaschen FP, Barr JW, Olson E, Honneffer J, Guard BC, et al. Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. J Vet Intern Med. 2020;34(5):1853-1866. 
  8. Lange K, Buerger M, Stallmach A, Bruns T. Effects of Antibiotics on Gut Microbiota. DDI. 2016;34(3):260-268. 
  9. Dudek-Wicher RK, Junka A, Bartoszewicz M. The influence of antibiotics and dietary components on gut microbiota. Gastroenterology Rev. 2018;13(2):85-92. 
  10. Menozzi A, Dall’Aglio M, Quintavalla F, Dallavalle L, Meucci V, Bertini S. Rifaximin is an effective alternative to metronidazole for the treatment of chronic enteropathy in dogs: a randomised trial. BMC Vet Res. 2016;12(1):217. 
  11. Duysburgh C, Van den Abbeele P, Morera M, Marzorati M. Lacticaseibacillus rhamnosus GG and supplementation exert protective effects on human gut microbiome following antibiotic administration. Benef Microbes. 2021;12(4):59-73.