Test the Microbiome

The Fecal Microbiome Vs The Gut Microbiome

The fecal microbiome refers specifically to the microorganisms present in fecal matter. This is in contrast to the widely used term, ‘gut microbiome’ that refers to the microorganisms that live along the entire digestive tract.

While the fecal microbiome is technically derived from the gut microbiome, the two terms are used interchangeably. This is due to standard practices in gut microbiome research, which use feces as a proxy for studying the broader microbial community of the gastrointestinal tract.

Many factors lead to fluctuations in the microbial makeup of the fecal microbiome, such as transit time and dietary changes. However, disease-states and dysbiosis of the gut microbiome are detectable regardless of fluctuations. For this reason, we use ‘gut microbiome analysis’ and ‘gut health test’ as surrogate terms for fecal microbiome analysis.

What Fecal Microbiome Analysis Can Tell You About Your Patient's Health

In both humans and animals, the gut microbiome—a community of trillions of bacteria and other microorganisms that live in the digestive tract— function to support numerous aspects of overall health, including proper digestion, absorption and a strong immune system.1

Different types of beneficial bacteria in the gut play different roles, and when there is an imbalance in the normal diversity of bacterial groups, the microbiome can’t perform all of its important functions. The result can be a variety of clinical signs, such as diarrhea, constipation, vomiting, bloating, atopy, obesity, and even behavioral or neurological symptoms.

Fecal microbiome testing can give you valuable information about what’s going on in your patient’s gut. Not only can it reveal bacterial imbalances that may be causing their clinical signs, but also highlight potential health problems before symptom-onset.

What Is Gut Microbiome Testing?

Gut microbiome testing is a way to detect dysbiosis and specific bacterial groups related to animal health. This can be determined with fecal microbiome analysis, which involves identifying the bacteria in the feces of an animal. While there are differences between the compositions of the fecal microbiome and the gut microbiome, feces has been shown to be an effective tool for determining gut microbiome health and a comprehensive diagnostic measure due to the mucosal membrane within the intestines.2,3

Fecal microbiome testing is accepted as a promising diagnostic tool. Studies using fecal microbiome analysis and a proxy for gut microbiome health have found that dysfunction or imbalance of the human microbiome is associated with a variety of conditions—including irritable bowel syndrome (IBS), Chron’s disease, colitis, inflammatory bowel disease (IBD), obesity, type 2 diabetes, anxiety, and depression. 4–10

Extensive research now focuses on the gut microbiome as a source of innovative treatments as well as new diagnostic approaches for these health conditions.11 In just the last few years, multiple healthcare companies have begun offering at-home microbiome test kits that allow people to learn about their own gut microbiome.

Although there’s still much to learn about the microbial ecosystem of the gut, fecal microbiome testing is a way to gain information about a patient’s gut health to help support a successful treatment plan and improve overall health.

Development of AnimalBiome Gut Health Testing

After realizing how many cats and dogs suffered from chronic diarrhea, digestive disorders, and atopy, AnimalBiome wanted to better understand how the microbiome was involved. Our founder, Holly Ganz, PhD, pioneered the first-ever at-home gut microbiome tests for cats and dogs.

Microbiome testing for Dogs and Cats: If your cat or dog has diarrhea or itchy skin problems they may have a bacterial imbalance.

Starting with a citizen-science project called KittyBiome, Holly and her collaborators put out a call for microbiome samples to study, offering each participant a detailed analysis of their pet’s gut bacteria. And with the help of many pet parents and their beloved four-legged friends, we were able to identify trends in prevalence of bacteria within a healthy gut of a healthy pet versus a gut of a clinical pet in a state of dysbiosis.

Your patient’s poop is about 50% microbes. A small sample of stool provides a lot of data about your patient’s unique gut microbiome.

AnimalBiome Has the Largest Database of Cat and Dog Microbiome Samples

Because of veterinarians like you, who want to utilize microbiome medicine and provide better health solutions for their patients, we have collected and analyzed more than 60,000 fecal samples from cats and dogs. Out of those, we have assembled a subset that meets our rigorous criteria for healthy animals. By studying those healthy samples, we’ve been able to build a subset of the specific bacterial taxa (groups) we can expect to find in the gut microbiome of a healthy cat or dog.

When a patient’s stool sample is submitted to our laboratory, we analyze the patient's fecal microbiome sample and cross reference it with our healthy data set. We then send you a detailed report, providing you with evidence-based dietary and supplement recommendations to improve gut microbiome health.

If your patient’s gut microbiome is already diverse and well balanced, it can look similar to the healthy reference set. But if not, the report will explain whether the solution is to add beneficial bacteria, remove pathogens, rebalance the existing populations, or a combination of approaches.

What Can I Learn About My Patient’s Health From Fecal Microbiome Testing?

Fecal microbiome testing provides useful insights that no other current veterinary test can offer. Clinical symptoms related to digestion, inflammation, abnormal physiological functions, improper immune system function, and other microbiome-associated conditions are likely indications of a gut microbiome dysbiosis.

AnimalBiome’s Gut Health test determines if and what bacterial dysbiosis is present, specific recommendations of how to address the dysbiosis, and actionable solutions to start the restoration process.

Antibiotics are known to cause both short- and long-term significant changes to the bacterial community in the gut microbiome of humans and animals alike.12 Antibiotics affect the gut microbiomes of individuals differently, so testing is a valuable tool to understand how the patient’s microbiome is impacted by antimicrobial therapy and what exactly is needed to restore it.

Here is what you can learn from microbiome testing with AnimalBiome’s Gut Health test:

Your Patient’s Unique Microbial Community

Using next-generation DNA sequencing, we identify 5000 different types of bacteria living in your patient’s gut, giving you a detailed picture of their unique gut microbiome.


If there are significant changes in the diversity and abundance in the gut microbes, the gut microbiome is out of balance, which may affect the physiological functions of the patient and ultimately alter their health status. Identifying imbalances early allows you to recommend important therapeutic recommendations that can improve or prevent symptoms.

Your Patient’s Optimal Diet

Each gut microbiome is unique. Different patients need different dietary adjustments to support the growth of specific beneficial bacteria. Food recommendations based on your patient’s individual results will help you make simple and effective dietary suggestions to improve your patient’s gut health and overall wellness.

Missing bacteria

A comparison of your patient’s results to the healthy canine or feline reference set will reveal whether your patient is missing key bacteria. Absences are often the result of antibiotic use, diet, illness, or multiple other factors.

Pathogenic Bacteria

Fecal microbiome testing can identify problematic groups of gut bacteria. Pathogenic bacteria, while in small amounts may be normal in a gut microbiome, can have unhealthy actions when they are able to flourish.

Get to Know Your Patient From the Inside Out

How It Works

Order A Gut Health Test Kit

Identify any imbalances in your patient’s gut microbiome. Order your kit in single or bulk test kits from our website www.animalbiome.vet.

Collect The Sample

The microbiome test kit includes everything you’ll need to collect a small sample of your patient’s stool. Collect 1 gram (the size of a pea) of fresh stool. Ideally, the stool is collected right from the rectum, but you can collect from freshly passed stool (<4 hours). If sampling from fresh stool, obtain a sample from the middle of the feces, so as to obtain a sample without contamination and less bacterial degradation.

There are different tests for cats and dogs. Be sure to use the correct species, and each patient will have 2 tubes with the same ID number. Once the sample is in the preservative solution, it can be kept at room temperature and is preserved for up to 1 year.

Once the sample is collected, complete the sample registration. First time users need to create an account in our Patient Portal. This site is where you add patient information and register the sample ID to the pet ID prior to sending the sample in.

Send The Sample

The bulk test kit includes return mailers. We offer 2-day Fed-Ex expedited shipping to our lab. You can print off these labels from within your patient portal.

Receive The Report

In 10-15 days, you’ll receive an email notification that your patient’s test results are ready and can be accessed via our online Patient Portal. You’ll receive a detailed report, complete with customized recommendations to improve your patient’s health.


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