Our pets’ health depends on more than the food they eat, the medications they receive, or the supplements in their bowls. In the mouth and GI tract lives a complex community of microorganisms that plays an important role in digestion, immune function, inflammation, and overall health. Integrative veterinary medicine recognizes that the body functions as an interconnected system. By combining conventional veterinary diagnostics with microbiome testing, targeted nutrition, prebiotics, probiotics, and other microbiome-supportive therapies, we can develop more individualized approaches to maintaining health and managing chronic disease.
What is the Microbiome, and Why Does it Matter?
The microbiome is the community of microorganisms that live in and on the body. These include bacteria, fungi, viruses, and other microscopic organisms, along with the genetic material and biological activity associated with them. Although the word bacteria often has a negative connotation, most microorganisms are harmless, or even beneficial. A healthy microbial community helps the body function normally and can protect against the effects of harmful organisms.
Two particularly important microbial communities are the gastrointestinal (GI) microbiome and the oral microbiome:
- The GI microbiome consists of microorganisms living throughout the digestive tract, particularly in the intestines. These organisms help break down components of food that the body cannot digest on its own, produce beneficial substances such as short-chain fatty acids, support the intestinal barrier, and influence immune system development and function. A balanced gut microbiome helps maintain normal stool quality, supports nutrient utilization, and contributes to the body’s ability to regulate inflammation. The gut and immune system communicate continuously, and the microorganisms living in the intestines are important participants in this relationship.
Beneficial gut bacteria also help limit the growth of undesirable microorganisms by competing for nutrients and space. When the microbial community becomes disrupted, this protective function may weaken. This disruption is called dysbiosis. It can involve a loss of beneficial microorganisms, an overgrowth of certain potentially harmful organisms, reduced microbial diversity, or changes in the relative abundance and activity of different microbial groups. Dysbiosis has been associated with chronic enteropathies, inflammatory bowel disease (IBD), diarrhea, and other digestive disorders. Research also suggests relationships between gut microbial changes and conditions involving the skin and immune system.
- The oral microbiome is the community of microorganisms living in the mouth, including on the teeth, gums, and tongue, and other oral surfaces. A healthy oral microbial community exists in balance with the surrounding tissues and helps maintain a stable environment. Problems can develop when the composition of this community changes and disease-associated organisms become more prominent. These changes can contribute to dental plaque, gingivitis, periodontal disease, and inflammation of the tissues supporting the teeth. The mouth is also an entry point to the digestive tract. Oral inflammation, periodontal disease, and the microorganisms associated with them can have implications beyond the mouth.
Why Balance Matters
The goal of microbiome support is not to eliminate all bacteria, or introduce as many beneficial organisms as possible. Instead, the objective is to encourage a diverse, stable microbial community that performs its normal functions, supporting the immune system and the body as a whole. Diet changes, stress, intestinal disease, medications, and other factors may influence the microbiome as well. An integrative approach looks at the whole patient, including diet, lifestyle, medical history, medications, clinical signs, and diagnostic findings. Microbiome testing can add another piece of information to this assessment and may help guide more individualized care.
Microbiome Testing
Microbiome testing is the first step to determine the different organisms living in your pet’s gut. These are easy, at-home tests that use tiny fecal samples to identify both healthy (“good”) and pathogenic (“bad) bacteria in the gut, which allows us to determine dietary and supplement options that are most effective for your pet. A microbial imbalance (also called “dysbiosis”) can be mild, moderate, or severe. If your pet is dealing with any of the following issues, microbiome testing can be an important first step: vomiting, diarrhea, weight loss, appetite changes, skin issues, suspected allergies, immune dysfunction, behavioral problems, bad breath, or dental disease.
We are proud to partner with AnimalBiome to offer at-home microbiome testing for dogs, cats, horses, and exotic pets. These tests are designed to provide information about microbial communities that may help guide decisions about nutrition and microbiome-supportive therapies. AnimalBiome’s Gut Microbiome Test analyzes a stool sample to assess the composition of the intestinal microbial community. The results can provide information about the relative abundance of selected bacterial groups, including beneficial organisms and organisms that may be associated with dysbiosis.
The test is performed using a sample collected at home according to the manufacturer’s instructions. Results are reviewed alongside the pet’s clinical history, diet, medication use, and other diagnostic findings. You can find more information about these tests (as well as order them online) here:
- GI Microbiome Test for Dogs
- GI Microbiome Test for Cats
- GI Microbiome Test for Horses
- GI Microbiome Test for Exotic Pets
AnimalBiome also offers an Oral Microbiome Test for dogs and cats. This test examines microorganisms associated with the oral environment and can provide additional information about a pet’s oral microbial profile. For pets with persistent bad breath, plaque accumulation, gingival inflammation, or recurring dental concerns, oral microbiome testing may offer another source of information to consider when developing a dental health plan.
Does My Pet Need Microbiome Testing?
Microbiome testing is essential for pets with any type of GI issues, such as vomiting, loose stools or diarrhea, constipation, weight loss, excessive gas, frequent bloody or mucousy stools, regurgitation, or appetite changes. Microbiome analysis may help identify patterns of dysbiosis that could be relevant to these symptoms. Depending on the findings, we may consider dietary adjustments, targeted microbial support, fiber supplementation, probiotics, or fecal microbiota transplantation as part of a broader treatment plan.
Other health issues that may benefit from microbiome testing include:
- Chronic skin issues (allergies, atopic dermatitis, recurrent itching, skin inflammation)
- Pets with a history of antibiotic use
- Chronic diseases
- Auto-immune disease
- Oral health issues (bad breath, visible plaque, red or bleeding gums, drooling, difficulty chewing, dropping food, pawing at the mouth, or changes in eating behavior)
Probiotics vs Prebiotics
Probiotics are live microorganisms that provide health benefits to the host. They are used to support gastrointestinal health and help maintain a balanced gut microbiome. Probiotics help support normal digestion, intestinal barrier function, and immune regulation. Certain strains may also help manage specific conditions, such as antibiotic-associated diarrhea or stress-related digestive upset. Common probiotic microorganisms used in veterinary products include species of Lactobacillus, Bifidobacterium, and Enterococcus, as well as the beneficial yeast Saccharomyces boulardii.
Prebiotics are substances that beneficial microorganisms (probiotics) can selectively use to support their growth or activity. In dogs and cats, prebiotics are commonly dietary fibers or other fermentable carbohydrates. Prebiotics promote the production of short-chain fatty acids, which helps nourish intestinal cells, support the intestinal barrier, and regulate immune function. They also help improve stool quality and support normal digestive function. Common prebiotics used in veterinary diets and supplements include fructooligosaccharides (FOS), mannanoligosaccharides (MOS), inulin, certain forms of resistant starch, and other fermentable fibers. Different prebiotics affect different microbial populations, so their benefits depend on the specific ingredient, dose, and individual animal
Microbiome Treatment Options
With microbiome test results in hand, we can determine what “good” bacteria we need to support, and what (if any) “bad” bacteria we need to get rid of. For pets with dysbiosis, we recommend rechecking the microbiome (using the microbiome test kits) after about 60 days of treatment. These results can be compared to initial results to evaluate your pet’s individual response to treatment, and allow for monitoring and amending treatment as needed.
- GUT RESTORE: Pets with severe or drastic microbiome imbalances may benefit from a fecal microbial transplant, also called FMT. This technique is a highly effective way to replace beneficial microbes directly into the GI tract, and jump start a healthy microbiome. These capsules must be given whole with food – do NOT open or crush capsules. Pets who are sensitive to new supplements should start slowly, giving 1 capsule every other day for 1-2 weeks, then gradually building up to the prescribed dose. If an adverse reaction occurs (such as loose stools), pause for 2-3 days and then restart with 1 capsule every other day. We will discuss your pet’s specific needs, but most dogs and cats need 30-60 days of FMT treatment, followed by a retest of the GI microbiome. FMT therapy is available for both dogs and cats:
GUT REBUILD: Pets with GI issues, dysbiosis, and/or a history of antibiotic use may benefit from Gut Rebuild – this supplement suppresses “bad” bacteria growth while supporting healthy, “good” bacteria growth and healing the gut wall. It can be used with FMT/Gut Restore in some cases as well.
Gut Rebuild capsules CAN be opened and mixed with food/treats, or given whole. These capsules can be given with or without food. Once the bottle is opened, store in a cool, dry place, but do not refrigerate/freeze. Do not give to pets with severe constipation. Pets who are sensitive to new supplements should start with 1 capsule per day, and slowly increase to prescribed dose. Maximum benefits of Gut Rebuild are seen after 30-60 days of continuous use.
GUT MAINTAIN: Pets with mild GI issues may benefit from Gut Maintain support. This supplement is a powerful blend of probiotics, prebiotics, and phages to support a robust, balanced, diverse, healthy gut microbiome. Gut Maintain capsules can be opened and mixed with food/treats, or given whole.
FIBER BIOME BLEND: For pets who need additional fiber in their diet, Fiber Biome Blend is an excellent option. This is a full-spectrum, food-grade blend of MOS, beet fiber, and larch arabinogalactan. This combination feeds beneficial bacteria along the length of the GI tract. Start introducing slowly to your pet’s diet over 1-2 weeks. This product contains organic beets, which may cause a harmless red color to the stools. Store in a cool, dry place. In humid environments, store in the refrigerator to reduce exposure to moisture.
DAILY DIGEST BLEND: Pets who need additional support to maximize digestion may benefit from digestive enzymes, such as those found in Daily Digest Blend. This is a full-spectrum blend of digestive enzymes that improve the bioavailability of nutrients from food. These enzymes help break down proteins, fats, fibers, and carbohydrates to make them easier to absorb. It is recommended for pets with food sensitivities, older pets, underweight animals, and those with digestive issues. The easy to use powder is added to the top of your pet’s food at each meal. First, add Daily Digest to a small amount of food that you know your pet enjoys before adding it to the rest of their meal.
The science of the microbiome continues to develop, and veterinary medicine is learning more about how microbial communities influence digestion, immune function, and inflammatory disease. These advances offer promising opportunities to personalize care. By combining thoughtful diagnostics, appropriate nutrition, targeted microbial support, and regular veterinary care, pet owners and veterinarians can work together to support a healthier gut, a healthier mouth, and better overall well-being.
To learn more about the magic of the microbiome, please visit Animal Biome. Specific items of interest include: