How to Test Your Gut Function and Evaluate Your Gut Health

Have you been experiencing digestive problems like bloating, gas, indigestion, or constipation? Or maybe something more serious like autoimmune disorders or chronic digestive inflammation? Gut health testing can help you better understand what’s going on in your gut, and how it's affecting the rest of your body.

Gut health tests evaluate the microbiome, absorption of nutrients, and digestive function to identify underlying gut infections, inflammation, food intolerances, and other gut issues. Poor gut health also negatively impacts mental health, the immune system, and overall health. Functional medicine doctors develop a personalized treatment plan for each patient based on their unique gut microbiome and digestive function.

Learn more about conditions we treat: Digestive disorders

There are a few different kinds of tests available, and your health practitioner will make recommendations based on your symptoms and medical history. Common gut health tests used to evaluate gut function and gut health include stool testing, breath tests, and blood testing.

Comprehensive GI assessment with stool tests

Stool testing can provide valuable information about your gut health. It involves collecting a small stool sample and looking at both the types and levels of bacteria, viruses, parasites, fungi, digestive enzymes, inflammation, and other gut health markers.

At CentreSpringMD, we use the advanced diagnostics of the GI Effects® Stool Profile, which provide quick, actionable clinical information for the management of gastrointestinal health. Utilizing cutting-edge technologies and biomarkers, this stool test is a valuable diagnostic tool that looks at 5 areas of overall digestive function:

  • Dysbiosis
  • Inflammation
  • Maldigestion (or malabsorption)
  • Metabolite imbalance
  • Infection

One stool sample can reveal important information about the root cause of many common gastrointestinal symptoms, such as gas, bloating, indigestion, abdominal pain, diarrhea, and constipation.

For insight into your digestive health, contact a patient care coordinator to get started.

What a gut health test measures

A stool test provides an accurate picture of each person's microbiome, in addition to inflammation produced by the immune system, underlying infections, and how well nutrients such as fat & protein are being absorbed. It can also identify:

  • Parasites, such as Giardia or intestinal worms
  • Bacterial infections such as Salmonella, C. diff, or H. pylori 
  • Viruses
  • Fungal infections, like Candida
  • The specific strains of bacteria in your gut microbiome

Stool testing relies on what are called biomarkers to obtain this information. These same biomarkers are also used to monitor clinical conditions, such as inflammatory bowel disease, food allergies, GI infections, pancreatic insufficiency, and malabsorption issues.

Related: H. Pylori Affects Half the Population—But Is It Harmful?

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Microbiome testing

Evaluate the amount and types of “good” and “bad” bacteria that make up your gut microbiome.

Good flora in your digestive system are responsible for producing short-chain fatty acids and other metabolic factors which protect your intestinal lining and provide fuel for cells in your colon. A microbiome test will look at these metabolites & SCFAs which make up a healthy gut.

Harmful bacteria, such as parasites and viruses, contribute to inflammatory activity that may lead to a leaky gut, hormone imbalance, or autoimmune disease. Microbiome tests using a stool sample determine how much and what types of potentially pathogenic bacteria reside in your gut. Examples of potentially harmful bacteria include H. pylori, Staphylococcus, Streptococcus, and E. coli.

Defend a healthy microbiome with a pre- or probiotic.

Digestive health testing

Ever wondered how well your gut is able to break down and absorb different nutrients, vitamins, or minerals? Stool tests can help provide insight into digestive function that may impact nutrient deficiencies, food intolerances, and malabsorption.

This involves measuring pancreatic enzymes, undigested protein in the colon, and how much fat is present in stool.

Stool testing also gives insight into how well you tolerate certain foods and may help identify food sensitivities or intolerances.

Read: Tips to Increase Nutrient & Vitamin Absorption

Multiple technologies identify which microbes reside in your GI tract

Genova’s GI Effects test uses a combination of PCR, culture, and microscopic methods to identify specific strains of microbes. Since a single technology cannot fully capture the dynamics of a constantly changing microbiome, this tests combines:

  • 16S rRNA gene polymerase chain reaction (PCR) amplification technique for anaerobic commensal bacteria
  • Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) technology for bacterial and fungal species identification via culture
  • Microscopic ova & parasites (O&P) detection
  • Real-time PCR for the identification of 6 common parasites 

Learn more about this test when you speak with a functional medicine provider.

Identify the root cause of digestive issues & disease

GI testing can look for various biomarkers associated with diseases that begin in the digestive system. 

Pancreatic issues

Stool samples are used to check for signs of digestive tract diseases like bile acid malabsorption and pancreatic insufficiency (1). 


One biomarker, calprotectin, has been proven clinically useful in differentiating between inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) (2). 

Allergies & intolerance

Eosinophil Protein X is a marker of inflammation and allergic response (3). 

Leaky gut

Fecal Secretory IgA is a marker of gut immunity and the health of the intestinal lining (4). 

Colon cancer

Some stool tests may also provide clinically relevant information to screen for signs of colon cancer (5).

Dealing with digestive issues, or symptoms of chronic inflammation? Find answers when you evaluate your gut health.

What happens during tests for gut health?

Most gut health tests require a sample of your stool, which is usually collected during an appointment with your healthcare provider. The sample is then sent to a laboratory for processing and analysis. There are at-home microbiome testing kits available, but they may not be as comprehensive or accurate as one ordered by your functional medicine practitioner.

Results will be returned to your doctor in the form of a report that outlines any bacterial overgrowth or imbalances in gut bacteria, as well as any infectious agents present, such as parasites and viruses.

Should you test your gut health?

Test results can help your healthcare provider develop a personalized treatment plan based on your unique gut microbiome, and how your gut is functioning.

Symptoms often improve as functional imbalances become normalized through diet, lifestyle, nutraceutical and/or pharmaceutical supplementation. Recommended interventions may include:

  • Antibiotic therapy
  • Anti-inflammatory protocols
  • Pancreatic/digestive enzyme therapy
  • Prebiotic and probiotics
  • Dietary changes
  • Herbal or natural therapies or supplements

Heal a leaky gut with functional medicine>>

Gut health testing and functional medicine

Understanding the vital role your digestive system plays in your overall health is key to improving quality of life and longevity. Testing is the first step in gaining insight into the health of your gut microbiome, and gives your healthcare provider an inside look at how to best support you. A functional approach that focuses on optimizing gut function rather than just symptom management creates lasting changes.

Talk to your healthcare provider if you’re interested in learning more about gut health testing.




gut health

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