What Is a Gut Health Test?
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Medically reviewed by Jay N. Yepuri, MD
A gut health test, also known as a gut microbiome test, identifies microbes like bacteria, fungi, and viruses in your gut. It can help give you a bigger picture of your gut health.
Gut health tests include blood tests and stool tests. Your healthcare provider might recommend them if you have digestive symptoms like diarrhea or bloating. These tests can also help diagnose infections and gastrointestinal (GI) conditions like colon cancer.
Gut tests can't identify all bacteria, but they can provide insight into microbes that might be causing symptoms and affecting your overall health.
What Is Your Gut Microbiome?
Your gut is your gastrointestinal system. It includes your stomach, intestines, and colon (large intestine). The gut microbiome balances 100 trillion beneficial and potentially harmful microbes that help maintain a healthy gut lining and digestion. A healthy microbiome is essential to overall health and may affect everything from mood to sleep to immunity.
An imbalanced gut microbiome, known medically as dysbiosis, can cause digestive symptoms like diarrhea and bloating. Dysbiosis is caused by an overgrowth of potentially harmful microbes and a decrease in beneficial microbes. It can also damage your gut lining, leading to inflammation as toxins and undigested food leak into your bloodstream and tissues.
Do You Need a Gut Health Test?
At-home gut health tests aren't necessary, but they can provide information about microbes in your gut.
Potential benefits of taking a gut health test may include:
Providing information on the balance of harmful and beneficial bacteria
Identifying specific harmful pathogens that can cause illness
Offering insights into how your gut microbiome balance may contribute to gut lining health, digestion, and inflammation
Research shows that people with certain gastrointestinal conditions often have an imbalanced gut microbiome. These conditions include:
Irritable bowel syndrome (IBS): A chronic condition that causes symptoms like diarrhea and constipation, which can flare at times
Inflammatory bowel disease (IBD): Inflammation in the GI tract, includes Crohn's disease and ulcerative colitis
Colorectal cancer: Cancer of the colon or rectum (the last part of the digestive tract, closest to the anus)
However, at-home gut health tests can't replace a diagnosis from a healthcare provider.
Types of Gut Health Tests
At-home gut health tests typically use deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sequencing to identify certain microbes from a stool sample. In a healthcare setting, providers may recommend stool tests that use DNA sequencing and microscopic examination.
Shotgun Metagenomic Sequencing (DNA Sequencing)
At-home gut health tests that use shotgun metagenomic sequencing look at gut bacteria and microbe DNA. DNA is like a blueprint that carries genetic information related to an organism. DNA sequencing is the most popular type of gut health testing.
Shotgun metagenomic sequencing can help identify harmful and beneficial gut microbes based on their unique DNA makeup. Shotgun metagenomics looks at the entire DNA content of the microbiome, which can help identify small numbers of microbes that are often missed.
Understanding a microbe's DNA also tells you how the microbe functions in your body. Gut health tests use this information to provide insight into your risk of certain gut-related conditions related to microbiome imbalances, digestive health, leaky gut, and inflammation. Leaky gut syndrome is a collection of symptoms based on the idea that the intestinal barrier is impaired, allowing toxins from the intestines to enter the bloodstream.
Shotgun metagenomic sequencing has a few downsides. It's expensive, and analyzing the information requires advanced technology used in a specialized lab.
Metatranscriptomics (RNA Sequencing)
Gut health tests examine the RNA in your gut microbiome with a technique called metatranscriptomics. RNA is a molecule in organisms and viruses that helps carry genetic information, or "instructions," needed for cells to function.
Identifying RNA molecules can help show the functional activity of microbes in your microbiome. In other words, it tells you how these microbes are behaving in your gut. If your microbiome is imbalanced, RNA can show potential harmful activities of microbes. RNA sequencing can also identify which microbes are actively affecting your gut health.
Understanding the RNA in your gut may show how microbes increase your risk of inflammation and other health issues. In addition, metatranscriptomics identifies overactive microbes that may be causing gut imbalance.
RNA sequencing offers even more information on your gut microbiome than DNA sequencing. However, like DNA sequencing, the testing is more challenging and more expensive than other gut health tests.
Clinical Stool Tests
Clinical stool tests analyze DNA from poop samples. Similar to at-home gut health tests, they can help identify microbes and microbiome imbalances in the gut. Unlike at-home gut tests, they're not used to give you an overview of gut microbes. Healthcare providers use stool tests to help diagnose infections, gastrointestinal diseases, and colon cancer.
A stool test can involve examining stool under a microscope or using other lab testing to identify pathogens and abnormal DNA. If you're sick, a stool test can help detect specific bacteria, viruses, and other pathogens causing your illness. Stool tests can also identify altered DNA that may be a sign of cancer.
In addition, a stool test can identify blood in your poop that indicates digestive tract bleeding. This can help diagnose conditions like:
Diverticulosis: A condition that occurs when small pockets on the lining of your intestines become inflamed or infected
Ulcerative colitis: A type of IBD that irritates the lining of your intestines
Stomach ulcers: Also called peptic ulcers, these are areas where the stomach lining is injured due to excess stomach acid
Colorectal cancer: Cancer of the colon or rectum
Stool tests must be ordered by a healthcare provider and cannot be purchased over the counter like an at-home test. However, they may be covered by your insurance.
How To Choose a Gut Health Test
Various at-home testing companies offer gut health tests, including Thorne, Viome, Zoe, and Tiny Health. Choosing the right at-home gut health test for you will depend on factors such as:
Reliability and accuracy: Look for companies that use CAP-accredited and CLIA-certified labs to make sure you choose a reputable and validated testing provider. These certifications mean the labs have regular inspections and meet quality standards for accurate results.
Time: You may need to wait 2-6 weeks for results, depending on the test you choose. Companies can also have a wait-time range, so you may wait more than a month for results. Some tests also connect directly to your smartphone via an app, potentially offering faster results as well as support.
Cost: Tests are not covered by insurance, but some are HSA- or FSA-eligible. They can cost as little as $100 but are usually closer to $200. Some companies require monthly subscriptions that can create lower short-term costs but higher long-term costs.
Ease of use: Collecting a sample with a swab or scoop may be more challenging for some people. If you need an easier method, look for tests that use a wipe to collect a sample.
Results: Some companies offer comprehensive results that tell you the specific nutrients, bacteria, fungi, and viruses in your stool. Other tests give you a vague overview of the imbalances of "good" and "bad" bacteria. Based on your results, many tests suggest ways to improve your gut health.
See your healthcare provider if you think you have a health condition related to your gut. They can determine if a stool test might help determine a diagnosis or at least rule out possible causes of your symptoms.
How To Take a Gut Health Test
An at-home gut health test involves taking a stool sample you send to a lab for testing. If you get the test from your healthcare provider, you may need to drop it off at a local lab within a certain time—for example, within two hours of taking the test.
Collecting your poop may seem a little unsanitary, but you won't touch the poop itself. You can also wear gloves. Stool samples are added to a specimen container that includes a preserving liquid. You likely won't need to store any stool in your refrigerator or freezer before sending your sample.
At-home gut health tests vary, but they typically include the following steps:
Activate your at-home test: If you receive the test in the mail from a company, there is usually an activation code on the back of your kit that you need to put into an app or online profile. From there, you may need to add specific health information, complete your profile, or fill out identification information for your stool specimen container.
Collect your stool: You'll need to pee before you collect a stool sample. Your healthcare provider or the test provider should provide some kind of sterile collection container, like a shallow pan, plastic bag, or hammock-like plastic wrap that you'll poop into. Some test providers provide you with a wipe instead of a container, in which case you will collect a small stool sample as you wipe your bottom.
Take a stool sample: If you are provided a stool collection container, you'll either use a provided small scooper or a swap to collect a small sample. You cannot collect stool directly from the toilet. Mixing stool with water or urine will lead to inaccurate results.
Transfer the sample to the specimen container: Place your stool samples into the provided container(s) or vial(s). You'll need to fill the containers with enough stool so that the liquid reaches the indicated fill line. Seal the containers or vials. If you use a wipe for the sample, you may be given a different container or sterile bag to store the sample.
Prepare the sample: Wash your hands after collecting your stool sample, prepare your sealed sample, and complete any necessary paperwork.
You will then mail or drop off your sample. If you're mailing the sample, you will typically be provided a prepaid shipping label and box to send your sample to the lab for testing. If you bring the sample to a local lab, you will need to put the date and time of sample collection on each container or vial. You will probably need to drop it off within several hours of taking the sample.
What Do Your Gut Health Test Results Mean?
You'll be given test results that identify possible pathogens, microbe imbalances, and risk factors for gut health issues.
Results included in your test results varies depending on the test provider. At-home gut health tests typically include test reports with the following markers or indicators:
Gut microbiome diversity: This identifies your gut's different bacteria, fungi, and viruses. Lower gut microbiome diversity is linked to conditions like diarrhea, IBD, liver disease, and Clostridiodes difficile (C. diff) infection—a bacterium that causes symptoms like diarrhea and colitis (colon inflammation).
Microbiome imbalance (dysbiosis): This tells you if you have an imbalance of helpful and harmful microbes in your gut. Dysbiosis can lead to digestive issues and increase your risk of gastrointestinal health conditions.
Micronutrients: This looks at the levels of essential micronutrients in your stool, which may indicate how your body processes and absorbs nutrients. Poor nutrient absorption can indicate gut issues like IBS. Micronutrients tested in at-home tests may include folate, vitamin B6, vitamin B12, and niacin.
Pathogens: This identifies viruses, bacteria, and parasites in your stool that can cause illness and digestive issues.
Intestinal permeability: This indicates how easily particles may pass through your intestinal barrier, which can indicate your risk of a leaky gut. A higher amount of harmful microbes often suggests a more permeable gut.
These markers don't necessarily give you actionable advice beyond changing your diet and lifestyle. Results from at-home testing companies may also push you to purchase company-produced supplements and health plans to "cure" your gut issues.
Considerations for Gut Health Tests
Gut health tests can provide valuable information, but they have their limitations.
Not Used To Diagnose Conditions
Researchers and healthcare providers still don't fully understand how to use gut microbiome information to create clinical treatment plans. As a result, at-home gut health tests cannot be used to diagnose any health conditions, and they are not approved by the FDA for accuracy or safety. They simply provide insight into the microbes in your stool and potential health risks associated with microbiome imbalances and pathogens.
Tests Can't Identify All Bacteria
Gut health tests can only identify a fraction of the bacteria found in stool. Just one gram of stool contains roughly 100 billion microbes, compared to the trillions in your gut, and current technology can't identify all of them. Therefore, gut health tests may not identify the microbes linked to your gut issues.
The Gut Microbiome Changes
The gut microbiome also changes frequently. This makes it challenging to identify a specific microbe imbalance from one test. Testing just a week later can result in very different results.
Cost
At-home gut health tests can become expensive because insurance does not cover them. Contact your healthcare provider if you have persistent gastrointestinal symptoms that affect your quality of life. They may recommend a stool test that can help diagnose underlying issues. They may also refer you to a gastroenterologist (a medical doctor who specializes in digestive health) for further evaluation and treatment.
Tips for Improving Your Gut Health
Your gut health is sometimes out of your control since genetics and infections can alter your gut microbiome. However, diet and lifestyle have significantly effect gut health.
Dietary and lifestyle changes that can help support a healthy gut microbiome include:
Eat more fiber: Eating fiber-rich foods helps your digestive tract keep things moving, promotes beneficial gut bacteria, and reduces your risk of gut-related health issues. Add more fiber to your diet with fruits, vegetables, whole grains, beans, nuts, and seeds.
Eat probiotic foods: Probiotics are microorganisms that help decrease harmful bacteria and increase good bacteria to improve your gut health. Probiotic foods include fermented foods like kefir, yogurt, kimchi, kombucha, sauerkraut, and tempeh.
Eat prebiotic foods: Prebiotics help feed probiotic bacteria to increase good bacteria growth. They also help change intestinal pH (acidity) to prevent harmful microbes from growing in your gut. Prebiotic foods include less ripe bananas, barley, asparagus, chicory, garlic, leeks, onions, and wheat bran.
Reduce sugar and ultra-processed foods: Foods that are ultra-processed or high in added sugar can decrease beneficial bacteria and increase inflammatory bacteria in your gut. Replacing these foods with more nutritious foods can help balance your microbiome.
Avoid smoking: Smoking cigarettes increases your intestinal pH, which allows more harmful bacteria to grow and increases your risk of developing digestive conditions like peptic ulcers and Crohn's disease.
Be mindful of alcohol: Heavy drinking can increase gut permeability and allow toxins to leak into your bloodstream (leaky gut). It can increase your risk of dysbiosis. People with chronic alcohol use often have more harmful bacteria compared to those who don't drink heavily.
Keep moving: Moving your body for at least 150 minutes a week can help you maintain a healthy gut. People with obesity risk factors—such as eating many processed foods and not engaging in regular physical activity—are more likely to have gut dysbiosis, gut permeability issues, and lower bacteria diversity in their gut. Research also shows that dysbiosis may contribute to obesity, so the link isn't fully understood. Weight is affected by a variety of biological, environmental, and social factors.
Probiotics: Foods vs. Supplements
Research shows that probiotic foods are generally more effective than probiotic supplements at supporting gut health. Probiotic foods contain other important nutrients and are processed more effectively by the body.
Supplements might also be resistant to stomach acid and bile salts—two key digestive liquids—as well as resistant to antibiotics.
A Quick Review
At-home gut health tests give you a bigger picture of the different microbes in your gut. This can help identify possible microbiome imbalances and risk factors for gut-related health conditions. However, it's important to remember that these tests are not diagnostic tools and cannot replace professional medical advice. At best, an at-home gut health test will give you more information that prompts you to live a healthier lifestyle.
See your healthcare provider if you have digestive issues that won't go away. They may order a stool test to look at specific cells and microbes in your gut. Depending on what microbes are flourishing in your gut, your healthcare may prescribe you a specific diet or treatment plan if you have a specific gut-related health condition.
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