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Using the GI Effects Test in Clinic

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Using the GI Effects Test in Clinic

Functional medicine providers utilize comprehensive stool testing as a cornerstone in their practice because it offers a deep and nuanced understanding of a patient's gastrointestinal health, reflecting the essential principle of addressing the root causes of health issues rather than merely treating symptoms. By delving into the intricacies of the gut microbiota, inflammation levels, and other markers of digestive function, these tests provide valuable insights into the complex interplay between gut health and overall well-being. The GI Effects Profile by Genova Diagnostics is a popular comprehensive stool testing option available for order through Rupa Health.


What Is the GI Effects Test?

The GI Effects panel is a highly customizable and comprehensive assessment of gut health. Genova Diagnostics utilizes PCR, stool culture, and microscopic testing methods to analyze stool samples and provide accurate and reliable data regarding three key functions of gut health: digestion/absorption, inflammation/immunology, and the gut microbiome.

Genova Diagnostics offers a Comprehensive and Fundamentals version of their GI Effects Profile. The provider can order a one-day or three-day stool collection with either version. Specific details outlining the differences between the GI Effects Comprehensive and GI Effects Fundamentals will be discussed later in this article, but the primary difference between the two is that the comprehensive panel includes a more extensive evaluation of the commensal gut bacteria.

Are There Certain Patients Who Would Benefit From the GI Effects Test?

A thorough evaluation of gut health will benefit patients struggling with digestive health. There is extensive evidence to support that imbalances in gut health and function lead to many gastrointestinal (GI) symptoms and conditions, including:

However, stool testing plays a greater role in medicine than solely investigating GI pathologies. The concept that extraintestinal disease originates in the gut is heavily backed by strong scientific evidence. Nutritional maldigestion and malabsorption will lead to nutritional deficiencies, manifesting as disease. Furthermore, the gut microbiome plays extensive roles in well-being beyond bowel functions. Prolonged dysbiosis has been linked to broader systemic complications and can manifest as and contribute to the development and severity of diseases, including:

What Information Does the GI Effects Test Tell Us?

The information on the GI Effects panels gives doctors and patients an ideal starting place for a root-cause assessment of GI complaints and other concerns related to GI health. The biomarkers measured with GI Effects can be categorized into three main groups pertaining to digestive health and function:


By including breakdown products of protein and fat in the test, healthcare professionals can gain valuable insights into the efficiency of the digestive process. Proteins are broken down into amino acids, and fats are broken down into fatty acids and other byproducts during digestion. Analyzing these breakdown products in stool samples helps identify malabsorption issues, which could stem from conditions such as enzyme deficiencies, food intolerances, or inflammatory bowel diseases. Healthcare providers can tailor their recommendations and treatments to address specific dietary deficiencies and promote overall GI well-being in patients by understanding how well the body is digesting and absorbing essential nutrients.

The GI Effects panels also include a marker called pancreatic elastase-1 (PE1), an enzyme secreted exclusively by the pancreas. PE1 is a specific and reliable marker for pancreatic exocrine function and is used to diagnose exocrine pancreatic insufficiency (EPI).


Genova Diagnostics utilizes three makers to identify the presence of intestinal inflammation, quantify the severity, and help diagnose and differentiate between different GI pathologies. This information guides appropriate diagnostic and treatment strategies and allows providers to noninvasively monitor treatment progress over time. 

Calprotectin is a marker of neutrophil-driven inflammation released from the intestinal mucosa into stool at sites of intestinal inflammation. Calprotectin helps distinguish between inflammatory and non-inflammatory bowel diseases (e.g., IBD vs. IBS). (20

Eosinophil protein X (EPX) is a marker of eosinophil-driven inflammation and allergic response. Elevations are most commonly associated with allergies and parasitic infections. (19

Fecal secretory IgA (sIgA) is included on the GI Effects Comprehensive panel, but not the Fundamentals. sIgA is the most abundant class of antibody in the intestinal lumen and is a marker of gut immunity and barrier function. Fecal sIgA is a non-specific immunological marker that can indicate the presence of infection, intestinal permeability, and immune hypersensitivity when elevated. (28

Occult blood refers to blood that is not visible to the naked eye, and its presence can indicate various gastrointestinal conditions, including ulcers, colorectal polyps, or even cancers in the digestive tract. The American College of Gastroenterology (ACG) recommends the fecal occult blood test as a preferred noninvasive testing alternative to colonoscopy for colorectal screening. (21

Gut Microbiome

Both the GI Effects Comprehensive and Fundamentals panels include metabolic indicators, including short-chain fatty acids (SCFAs) and beta-glucuronidase, to demonstrate vital metabolic functions performed by the commensal microbiota. Additionally, both panels have bacterial and mycology (fungal) cultures to assess the presence of beneficial and pathogenic organisms.

For a more comprehensive evaluation of the commensal makeup of the gut microbiome, consider ordering the GI Effects Comprehensive panel over the Fundamentals. This panel also utilizes PCR technology to assess 24 commensal bacterial species and microscopic and PCR evaluation for parasitic infections. 

Additional Add-On Tests

The GI Effects panels are highly customizable. Depending on the needs of the patient, providers can choose to add any of the following tests to either test panel:

  • Screening for infectious agents: Campylobacter, Clostridium difficile, Escherichia coli, and Helicobacter pylori
  • Fecal lactoferrin 
  • Macroscopic examination for worms
  • Zonulin family peptide
  • KOH preparation for yeast

How to Use the GI Effects Test in Clinic

The decision to choose the Comprehensive or Fundamentals panel will be determined based on cost, patient symptoms, and the depth of information required for evaluation. Selection of the one-day or three-day sample collection is based on the doctor's suspicion of parasitic infection. In cases of no/low suspicion, a one-day sample will likely be adequate; for high suspicion, providers should order the three-day collection kit.

With so many comprehensive stool tests on the market, you may wonder, "Why choose this one over others?" The GI Effects provides a broad overview of the three main elements of GI health and is highly customizable depending on your patient's needs. One of the appeals of Genova Diagnostics is its user-friendly results report. The first page of their reports includes functional imbalance scores for the following categories: maldigestion, inflammation, dysbiosis, metabolic imbalance, and infection. These scores are rated on a scale from 0-10 and color-coded to help patients and providers easily determine the areas of gut health that require the most attention. Additionally, the report overview includes therapeutic support options under each category to serve as potential treatment ideas.

Genova Diagnostics also includes inflammation-associated dysbiosis and methane dysbiosis scores in their tests. The inflammation-associated dysbiosis (IAD) score is a metric used to assess the relationship between intestinal inflammation and the composition of the gut microbiota. This score is significant because it provides valuable information about how inflammation in the gastrointestinal tract influences the balance of beneficial and harmful bacteria in the gut. The methane dysbiosis score is a metric used to assess the levels of methane-producing microorganisms (archaea) in the gut, which have been associated with small intestinal bacterial overgrowth (SIBO) and constipation-predominant IBS. 

Functional medicine doctors use comprehensive stool test results as a foundational tool in providing holistic healthcare and developing individualized treatment plans. Comprehensive stool tests allow functional medicine doctors to create personalized treatment plans tailored to the patient's specific microbial composition and imbalances. This might involve referral to a gastroenterologist for advanced imaging, dietary modifications, probiotic or prebiotic supplementation, digestive enzyme support, or antimicrobial therapies to restore a healthy balance of gut bacteria. Not only are stool tests diagnostic, but they also serve as a tool for monitoring progress to track changes in digestion, inflammation, and microbial composition as therapeutic interventions are implemented. 

Labs to Consider for Further Refinement of Treatments

In some cases, results gathered from the GI Effects panel will indicate the need for further testing. Genova Diagnostics offers a variety of additional panels that can be helpful to pair with the GI Effects tests to evaluate intestinal health more thoroughly. 


Microbiomix is available as a stand-alone profile or add-on to the GI Effects Comprehensive Profile. It uses gold-standard metagenomic shotgun/whole genome sequencing to provide increased detection of over 28,000 species of bacteria, fungi, protists, and archaea, as well as unique microbial metabolites that would not otherwise be detected on the standard GI Effects panel. 

SIBO Breath Test

SIBO is a commonly overlooked digestive condition characterized by bacterial overgrowth in the upper digestive tract that frequently causes IBS and other digestive symptoms. Comprehensive stool testing cannot diagnose SIBO, but specific results (such as increased sIgA or methane dysbiosis scores), along with the patient's clinical presentation, may suggest its presence. SIBO can be diagnosed with an at-home breath test that measures various gaseous byproducts of bacterial fermentation. Genova Diagnostics offers two testing options: a 2-hour and 3-hour lactulose breath test. The 3-hour test is preferred for patients with chronic constipation, slowed intestinal motility, and suspected intestinal methanogen overgrowth.


Patients with inflammatory bowel diseases, significant malabsorptive conditions, or restricted diets due to GI symptoms are at risk for multiple nutritional deficiencies. The NutrEval is Genova Diagnostic's most comprehensive nutritional assessment of over 125 organic acids, oxidative stress, amino acids, fatty acids, micronutrients, and toxic elements to screen for nutritional deficiencies and insufficiencies. Results can help doctors tailor targeted dietary and supplemental recommendations to ensure patients maintain optimal nutritional status. Genova offers two versions of this test: NutrEval Plasma and NutrEval FMV

Intestinal Permeability

Urine lactulose-mannitol testing is used to screen for intestinal permeability. In this test, patients are given a solution containing two sugars: lactulose and mannitol. After the patient drinks the solution, urine samples are collected and analyzed. Elevated levels of lactulose in the urine indicate increased intestinal permeability, suggesting that the intestinal barrier is compromised and allowing larger molecules to pass through. By assessing the ratio of lactulose to mannitol in the urine, healthcare professionals can evaluate the integrity of the intestinal lining. This test is valuable in diagnosing conditions associated with "leaky gut."



The GI Effects stool test stands as a valuable tool in functional and personalized healthcare, offering a comprehensive and detailed insight into the intricate workings of the gastrointestinal system. Its measurement of key intestinal biomarkers helps doctors and their patients understand the root cause of various health concerns and craft highly individualized and effective treatment strategies.

Learn More About the GI Effects Test

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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