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When To Order A Stool Test For Your Patients

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When To Order A Stool Test For Your Patients

In the United States, digestive symptoms have become increasingly prevalent, affecting up to 70 million Americans. While these symptoms are commonly associated with gastrointestinal (GI) disorders, emerging evidence suggests that gut health imbalances might contribute to various health complaints extending beyond digestive symptoms. Even in the absence of overt GI symptoms, disturbances in the gut microbiome have been implicated in systemic health conditions. The growing body of research underscores the pivotal role of the gut in human health, influencing not only digestive well-being but also systemic functions. Against this backdrop, stool tests have emerged as indispensable diagnostic tools in conventional and functional medicine for comprehensively assessing gut health.


Overview of Stool Testing

Stool tests are non-invasive testing methods that provide valuable insights into various aspects of GI health. This non-invasive procedure involves the analysis of fecal samples to measure desired biomarkers regarding GI health and function. 

Stool culture refers to the inoculation of agar plates with a fecal sample to grow out and identify pathogenic GI bacteria. The Campylobacter/Salmonella/Shigella test by Access Medical Laboratories is an example of a stool culture commonly ordered for patients with acute diarrhea to rule out infection by the common bacterial culprits responsible for gastroenteritis. Culture testing methods are also used to identify intestinal fungal overgrowth; for example, the Yeast Culture by Genova Diagnostics will identify yeast growing in the gut and includes a sensitivity panel for any isolated species to guide treatment decisions.

Ova & parasite (O&P) testing, such as the O&P with Permanent Stain by Access Medical Labs,  detects whether parasites and their eggs are present in a stool sample by analyzing it under a microscope. False negatives are common with single-collection O&P tests, so an O&Px3, in which three stool samples are collected on separate days, is recommended when testing for parasitic infections.

Comprehensive digestive stool analysis (CDSA), such as the Comprehensive Stool Analysis by Mosaic Diagnostics, represents a more holistic approach to evaluating GI health. This multifaceted test assesses various parameters, including the balance of beneficial and harmful bacteria, digestive enzyme activity, intestinal inflammation markers, and a gut microbiome profile. By examining these diverse aspects, healthcare professionals can gain a nuanced understanding of the patient's digestive function, paving the way for personalized treatment strategies that address the underlying causes of GI disorders.

The Role of Stool Testing in Functional Medicine

Functional medicine brings a distinctive approach to understanding gut health, emphasizing the interconnectedness of various bodily systems and the role of the gut in overall well-being. Stool testing is a key diagnostic tool in functional medicine, providing practitioners with valuable insights into the intricate dynamics of the gut microbiome, digestive function, and their implications for broader health.

Optimal gut health is synonymous with efficient digestive function. A balanced and diverse gut microbiome supports breaking down complex carbohydrates and fibers that the body can't digest on its own. During this process, bacteria produce digestive byproducts called short-chain fatty acids (SCFAs), which are vital for human health. SCFAs serve as a primary energy source for colonocytes, maintain a healthy gut barrier, and exert anti-inflammatory effects, influencing various aspects of metabolic and immune function. Poor gut health, on the other hand, has been correlated with digestive concerns such as irritable bowel syndrome (IBS), bloating, and irregular bowel movements. 

A robust immune system is intricately linked to the health of the gut. Stool testing has unveiled associations between imbalances in the gut microbiome and compromised immune function. Poor gut health is linked to an increased susceptibility to infections, autoimmune conditions, and cancer.

Gut dysbiosis and intestinal inflammation have been consistently correlated with inflammatory conditions and chronic disease. Chronic intestinal inflammation is implicated in developing GI conditions like inflammatory bowel disease (IBD), gastritis, and diverticulitis. However, emerging evidence also suggests that poor gut health is also involved in more systemic conditions, such as cardiovascular disease, obesity, and advanced cognitive decline.  

The gut-brain axis, a bidirectional communication system between the gut and the brain, underscores the impact of gut health on mental and emotional well-being. Stool testing has revealed connections between gut dysbiosis and mental health disorders such as anxiety and depression. 

The integration of comprehensive stool testing into clinical practice offers unparalleled benefits. By uncovering specific imbalances in the gut microbiome, digestive function, and inflammatory markers, practitioners can tailor interventions to each patient's individual needs. This personalized approach enhances the precision of therapeutic strategies, addressing the root cause of health concerns rather than merely alleviating symptoms. Stool testing emerges as a cornerstone in the functional medicine paradigm, providing clinicians with a holistic understanding of a patient's health and guiding interventions that extend beyond symptom management to promote enduring systemic well-being.

Indications for Stool Testing

Digestive symptoms indicative of an unhealthy gut that warrant stool testing include persistent diarrhea, chronic constipation, abdominal pain, bloating, excessive gas, heartburn/reflux, bad breath, unexplained weight loss, food intolerances, and the presence of undigested food in the stool. These symptoms may suggest imbalances in the gut microbiome, inflammation, malabsorption issues, or increased intestinal permeability ("leaky gut"). Stool testing is a valuable diagnostic tool for uncovering underlying causes of symptoms and guiding targeted interventions for optimal gut health.

Extraintestinal symptoms and conditions that have been linked to dysbiosis, indicating the need for comprehensive stool testing as part of a thorough evaluation, include:

Stool tests can act as a non-invasive testing method to help distinguish between bowel pathologies and guide doctors in decision-making during the diagnostic evaluation process of GI symptoms. For example, calprotectin is a protein neutrophils release in response to GI inflammation. IBS and IBD often present with similar symptoms, making it difficult to distinguish them based on clinical presentation alone. Fecal calprotectin, a test that can be ordered through Diagnostic Solutions, can help differentiate between IBS and IBD. Patients presenting with IBS symptoms and a fecal calprotectin of less than 40 μg/g have less than a 1% chance of having IBD. Conversely, fecal calprotectin levels greater than 50 μg/g indicate intestinal inflammation caused by IBD, celiac disease, colon cancer, diverticulitis, chronic use of anti-inflammatory drugs, and intestinal infections. (26

Preparing Patients for a Stool Test

Following specific instructions when preparing for a stool test will ensure accurate results. Different stool tests may have slight variations in preparation and collection instructions, so it is always important to read the test kit instructions thoroughly before beginning the stool collection. If you have concerns or questions, consult with your healthcare provider or the testing facility for clarification before collecting stool specimens. 

In general, patients should follow these instructions before collecting stool samples:

  • Discontinue using supplements such as digestive enzymes, probiotics, antibiotics, or antifungal supplements for at least one week before the test, as these can influence the composition of your gut microbiome. 
  • Adjust medication as advised by your healthcare provider, particularly avoiding medicines that may impact digestive function, such as antidiarrheal medications or laxatives. Never discontinue a medication before first consulting with your doctor.
  • Maintain a regular diet for at least two days before the test, avoiding drastic changes in dietary habits to provide a representative sample of your digestive function. Stay adequately hydrated in the days leading up to the test.
  • Use the provided collection container to catch a stool sample during a bowel movement, avoiding contact with toilet water or cleaning agents. Do not mix urine or water with the sample, and fill the container to the indicated fill line. Wash your hands thoroughly before collection to prevent contamination. 
  • Send the sample to the testing facility promptly, following their specific instructions for storage and transportation. Complete any required paperwork with accurate details about the date and time of collection. 

Interpreting Stool Test Results

A comprehensive stool test evaluates parameters such as microbial composition, digestive function, and inflammatory markers. Normal findings typically encompass a balanced and diverse gut microbiome, efficient digestive enzyme activity, and minimal levels of inflammatory markers. Discussed below are common abnormalities that one may find on a CDSA. 


An intestinal infection results from harmful microorganisms, such as bacteria, parasites, viruses, or yeast, that actively invade and multiply in the intestines. These invaders can lead to inflammation, disrupt normal digestive processes, and cause symptoms like diarrhea, abdominal pain, and fever. Infections are often acute and require targeted treatments such as antibiotics or antiparasitic medications to eliminate the causative agents. Examples of common pathogenic microorganisms that cause GI infections include Salmonella, E. coli, norovirus, Giardia, and Candida. (27


Dysbiosis is an imbalance in the composition and diversity of the gut microbiota. Dysbiosis can be classified as a loss of beneficial microorganisms (e.g., Lactobacillus and Bifidobacterium), an overgrowth of harmful organisms (e.g., Clostridium), and/or a loss of microbial diversity. This imbalance can result from various factors, including antibiotic use, dietary choices, or other lifestyle factors. 


Markers of inflammation, such as calprotectin and lactoferrin, provide insights into the immune response within the GI tract. Elevated levels of these markers may suggest inflammatory conditions like IBD. Identifying and addressing inflammation is crucial for preventing long-term damage and managing associated symptoms effectively. (10


A CDSA can unveil various findings indicative of malabsorption, reflecting deficiencies in nutrient absorption within the GI tract. Elevated levels of undigested fat in the stool suggest inadequate breakdown and absorption of fats, potentially signaling issues with pancreatic enzyme function or bile acid secretion. Reduced levels of pancreatic enzymes, such as elastase and chymotrypsin, in stool samples may signify pancreatic insufficiency. Abnormal stool pH levels can point to imbalances in the digestion and absorption of carbohydrates, impacting the GI environment. Zonulin is a marker associated with intestinal permeability; increased levels may suggest impaired gut barrier function, potentially contributing to malabsorption and the passage of larger molecules through the intestinal lining.

Integrating Stool Test Results Into Patient Care

Stool test results serve as a valuable guide for personalized treatment decisions, offering insights that can inform interventions tailored to the individual's unique gut health profile. The results facilitate a root-cause treatment approach, helping doctors to incorporate targeted strategies such as additional diagnostic testing, prescription or natural antimicrobials, probiotics and prebiotics, gut-healing supplements, dietary modifications, and other lifestyle changes. Personalized treatment plans align with the principles of functional medicine, considering both the specific test findings and the patient's broader clinical context.


When to Order a Stool Test: Final Thoughts

Stool testing holds immense value in healthcare, serving as a tool in diagnosing and managing GI issues. Comprehensive stool testing offers practitioners a nuanced understanding of the gut microbiome, digestive function, and inflammation, supporting a holistic approach to medicine tailored to patients' needs. By integrating stool testing into their clinical practice and diagnostic arsenal, healthcare practitioners can foster personalized patient care and enable precise interventions that contribute to the overarching goal of restoring and maintaining optimal health. Embracing stool testing in the clinical setting helps practitioners navigate the intricate landscape of GI health with greater accuracy and efficacy, ultimately enhancing patient outcomes.

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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