Medical Policy

Policy Num:       11.001.034
Policy Name:     Fecal Analysis in the Diagnosis of Intestinal Dysbiosis
Policy ID:           (11.001.034]  [Ac / B+ / M- / P-]  [2.04.26)

Last Review:      January 08, 2025
Next Review:      January 20, 2026
 

Related Policies:

02.001.076 - Fecal Microbiota Transplantation
11.003.080- Fecal Calprotectin Testing

Fecal Analysis in the Diagnosis of Intestinal Dysbiosis

Summary

Description

Intestinal dysbiosis may be defined as a state of disordered microbial ecology that is believed to cause disease. Laboratory analysis of fecal samples is proposed as a method of identifying individuals with intestinal dysbiosis and other gastrointestinal disorders.

Summary of Evidence

For individuals with gastrointestinal conditions such as suspected intestinal dysbiosis, irritable bowel syndrome (IBS), malabsorption, or small intestinal bacterial overgrowth who receive fecal analysis testing, the evidence includes several cohort and case-control studies comparing fecal microbiota in patients who had a known disease with healthy controls. The relevant outcomes are test validity, symptoms, and functional outcomes. The available retrospective cohort studies on fecal analysis have suggested that some components of the fecal microbiome and inflammatory markers may differ across patients with IBS subtypes. No studies were identified on the diagnostic accuracy of fecal analysis versus another diagnostic approach or that compared health outcomes in patients managed with and without fecal analysis tests. No studies were identified that directly informed the use of fecal analysis in the evaluation of intestinal dysbiosis, malabsorption, or small intestinal bacterial overgrowth. The evidence is insufficient to determine that the technology results in an improvement in the net health outcome.

Additional Information

Not applicable.

Objective

The objective of this evidence review is to determine whether the use of fecal analysis in the management of a variety of intestinal disorders improves the net health outcome.

Policy Statements

Policy Guidelines

Benefit Application

Background

Fecal Markers of Dysbiosis

Laboratory analysis of both stool and urine has been investigated as markers of dysbiosis. Commercial laboratories may offer testing for comprehensive panels or individual components of various aspects of digestion, absorption, microbiology, and metabolic markers. Representative components of fecal dysbiosis testing are summarized in Table 1.

Table 1. Components of the Fecal Dysbiosis Marker Analysis

    a Fecal calprotectin as a stand-alone test is addressed in evidence review 2.04.69.

A related topic, fecal microbiota transplantation, the infusion of intestinal microorganisms to restore normal intestinal flora, is addressed in evidence review 2.01.92. Fecal microbiota transplantation has been rigorously studied for the treatment of patients with recurrent Clostridioides difficile infection.

Regulatory Status

Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; laboratory-developed tests must meet the general regulatory standards of the Clinical Laboratory Improvement Amendments. Laboratories that offer laboratory-developed tests must be licensed by the Clinical Laboratory Improvement Amendments for high-complexity testing. To date, the U.S. Food and Drug Administration has chosen not to require any regulatory review of comprehensive testing for fecal dysbiosis.

Some U.S commercially available fecal dysbiosis tests are listed below in Table 2.

Table 2. Commercially Available Fecal Dysbiosis Tests by CLIA Certified Laboratories

    CLIA: Clinical Laboratory Improvement Amendments

Rationale

This evidence review was created in November 2001 and has been updated regularly with searches of the PubMed database. The most recent literature update was performed through October 22, 2024.

Evidence reviews assess whether a medical test is clinically useful. A useful test provides information to make a clinical management decision that improves the net health outcome. That is, the balance of benefits and harms is better when the test is used to manage the condition than when another test or no test is used to manage the condition.

The first step in assessing a medical test is to formulate the clinical context and purpose of the test. The test must be technically reliable, clinically valid, and clinically useful for that purpose. Evidence reviews assess the evidence on whether a test is clinically valid and clinically useful. Technical reliability is outside the scope of these reviews, and credible information on technical reliability is available from other sources.

Promotion of greater diversity and inclusion in clinical research of historically marginalized groups (e.g., People of Color [African-American, Asian, Black, Latino and Native American]; LGBTQIA (Lesbian, Gay, Bisexual, Transgender, Queer, Intersex, Asexual); Women; and People with Disabilities [Physical and Invisible]) allows policy populations to be more reflective of and findings more applicable to our diverse members. While we also strive to use inclusive language related to these groups in our policies, use of gender-specific nouns (e.g., women, men, sisters, etc.) will continue when reflective of language used in publications describing study populations.

Population Reference No. 1

Fecal Testing for Intestinal Dysbiosis

The gastrointestinal tract is colonized by a large number and a variety of microorganisms including bacteria, fungi, and archaea. The concept of intestinal dysbiosis rests on the assumption that abnormal patterns of intestinal flora, such as overgrowth of some commonly found microorganisms, have an impact on human health. Symptoms and conditions attributed to intestinal dysbiosis in addition to gastrointestinal disorders include chronic disorders (eg, irritable bowel syndrome [IBS], inflammatory or autoimmune disorders, food allergy, atopic eczema, unexplained fatigue, arthritis, ankylosing spondylitis), malnutrition, or neuropsychiatric symptoms or neurodevelopmental conditions (eg, autism), and breast and colon cancer.

The gastrointestinal tract symptoms attributed to intestinal dysbiosis (ie, bloating, flatulence, diarrhea, constipation) overlap in part with either IBS or small intestinal bacterial overgrowth syndrome. The diagnosis of IBS is typically made clinically, based on a set of criteria referred to as the Rome criteria. The small intestine normally contains a limited number of bacteria, at least as compared with the large intestine. Small intestine bacterial overgrowth may occur due to altered motility (including blind loops), decreased acidity, exposure to antibiotics, or surgical resection of the small bowel. Symptoms include malabsorption, diarrhea, fatigue, and lethargy. The laboratory criterion standard for diagnosis consists of the culture of a jejunal fluid sample, but this requires invasive testing. Hydrogen breath tests, commonly used to evaluate lactose intolerance, have been adapted for use in diagnosing small intestinal bacterial overgrowth.

Clinical Context and Test Purpose

The purpose of fecal analysis in patients who have various gastrointestinal conditions is to differentiate intestinal microflora and related immunologic responses that may be related to those conditions.

The following PICO was used to select literature to inform this review.

Populations

The relevant population of interest is those with gastrointestinal conditions such as suspected intestinal dysbiosis, IBS, malabsorption, or small intestinal bacterial overgrowth.

Interventions

The intervention of interest is the use of fecal dysbiosis testing. The rationale for intestinal dysbiosis testing is that alterations in intestinal flora (eg, overgrowth of some commonly found microorganisms) and related immunologic responses have an impact on human health and disease. The further assumption is that therapeutic (antibiotics, prebiotic, probiotic, or fecal microbiota transplantation) or lifestyle management interventions can be made to address the alterations.

Comparators

The following practices are currently being used to manage various gastrointestinal conditions: the standard approach to diagnosing specific intestinal conditions, which can include using laboratory tests, imaging, and endoscopy as indicated.

Outcomes

The general outcomes of interest are the correct diagnosis of gastrointestinal conditions potentially associated with alterations in intestinal microflora and initiation of appropriate treatment.

These tests might be used during the evaluation and treatment of acute and chronic intestinal disorders. The duration of follow-up is condition-specific and is expected to be weeks to months  later.

Study Selection Criteria

For the evaluation of clinical validity of fecal dysbiosis testing, methodologically credible studies were selected using the following principles:

For the evaluation of the clinical validity of the tests, studies that meet the following eligibility criteria were considered:

• Reported on the accuracy of the marketed version of the technology (including any algorithms used to calculate scores)

• Included a suitable reference standard

• Patient/sample clinical characteristics were described

• Patient/sample selection criteria were described

• Included a validation cohort separate from the development cohort.

Clinically Valid

A test must detect the presence or absence of a condition, the risk of developing a condition in the future, or treatment response (beneficial or adverse).

Review of Evidence

Establishing that fecal analysis to identify intestinal dysbiosis is beneficial would involve evidence that the fecal dysbiosis testing provides an incremental benefit to net health outcomes in patients with gastrointestinal tract symptoms as compared to current clinical pathways. No studies were identified that compared health outcomes in individuals managed with and without fecal analysis to identify intestinal dysbiosis. There were also no studies on the accuracy of fecal analysis vs another method for diagnosing IBS, small intestine bacterial overgrowth, or other conditions. Additionally, no studies were identified establishing diagnostic criteria for intestinal dysbiosis as a disorder.

Retrospective Studies

Emmanuel et al (2016) retrospectively analyzed fecal biomarker results, dichotomized to normal or abnormal, from 3553 patients who underwent stool testing and met Rome III symptom criteria for IBS.^1, Records were identified from samples sent to Genova Diagnostics from 2013-2014 for which patient questionnaires were completed (patient questionnaires are sent with every test kit; demographic surveys were completed for 7503 of 24258 of the fecal specimens obtained during study period, and Rome III questionnaire results were completed for 5990 of those) and the case definition of IBS was based on patient reporting of symptoms on the Rome III questionnaire. The Genova Comprehensive Digestive Stool Analysis evaluates digestion/absorption markers, gut metabolic markers, and gut microbiology markers.^2, Of the 3553 patient samples included, 13.6%, 27.5%, and 58.1%, respectively, reported having constipation-predominant IBS, diarrhea-predominant (IBS-D), and mixed subtypes of IBS. Most patients (93.5%) had at least 1 abnormal result. There were differences by IBS subgroup, with IBS-D patients demonstrating higher rates of abnormal fecal calprotectin, eosinophil protein X, and bacterial potential pathogens (13.4%, 12.2%, and 75% of subjects, respectively) than constipation-predominant IBS patients (7.1%, 4.4%, and 71.0%, respectively) and mixed subtypes of IBS patients (10.9%, p<0.004 vs IBS-D; 8.0%, p<0.003 vs IBS-D; 71.6%, p=0.010 vs p IBS-D).

A retrospective analysis of data from the Genova Diagnostics database for 2256 patients who underwent stool testing was published by Goepp et al (2014).^3, Patients had symptoms suggestive of IBS (eg, 48% had abdominal pain, 14% had diarrhea). Eighty-three percent of patients had at least 1 abnormal test result. The most common abnormal result, occurring in 73% of cases, was low growth in the beneficial bacteria lactobacillus and/or bifidobacterium. The next most common was testing positive for eosinophil protein X and fecal calprotectin, occurring in 14% and 12% of samples, respectively. A limitation of the study was that it did not include a confirmation of the diagnosis of IBS (ie, using Rome criteria) and thus the accuracy of the Genova tests compared with clinical diagnosis could not be determined.

Nonrandomized Observational Studies

Studies using quantitative real-time polymerase chain reaction analysis have compared microbiota in patients who had known disease with healthy controls in an attempt to identify a microbiotic profile associated with a particular disease. None of these studies evaluated whether the fecal analysis in patients with IBS or other conditions led to improved health outcomes.

Jeffrey et al (2020) evaluated fecal samples of 80 patients with IBS and 65 healthy controls.^4,Ruminococcus gnavus and Lachnospiraceae species were significantly elevated in patients with IBS, while Barnesiellaintestinihominis and Coprococcus catus amounts were found to be significantly lower. Additionally, in IBS patients, galactose degradation, sulfate reduction and assimilation, and cysteine biosynthesis were all reduced, indicating a decrease in sulfur metabolism compared to controls. No differences were noted in fecal microbiota across IBS subtypes. In patients screened for bile acid malabsorption (n=45), 40% tested positive to varying degrees. Only patients with positive screening results in the severe bile acid malabsorption (BAM) category showed significant differences in their fecal microbiome compared to borderline, mild, and moderate cases. Elevated glycerophospholipids and oligopeptides were considered predictive for BAM.

Andoh et al (2012) reported on fecal microbiota profiles of 161 Japanese patients with Crohn disease (CD) and 121 healthy controls.^5, Healthy individuals tended to have a different distribution of fecal microbiota than CD patients. For example, compared with controls, CD patients had significantly lower levels of Faecalibacterium and Eubacterium and significantly higher levels of Streptococcus.

Sobhani et al (2011) evaluated fecal microbiota samples taken before colonoscopy from 60 patients with colorectal cancer and 119 sex-matched healthy individuals in France.^6, Total bacteria levels did not differ significantly between colorectal cancer and non-colorectal cancer groups. There were significant elevations of the Bacteroides/Prevotella group in the colorectal cancer population.

Joossens et al (2011) published a study comparing fecal microbiota in 68 patients with CD, 84 unaffected relatives, and 55 matched controls in Belgium.^7, When samples from patients who had CD were compared with all unaffected controls, significant differences were found in the concentration of 5 bacterial species. Compared with controls, CD patients had lower levels of Dialister invisus, an uncharacterized species of Clostridium cluster XIVa, Faecalibacterium prausnitzii, and Bifidobacterium adolescentis as well as an increase in Ruminococcus gnavus.

Fecal markers in addition to microbiology profiles have evaluated whether the testing can distinguish between individuals with various gastrointestinal diseases. Langhorst et al (2008) in Germany evaluated 139 patients (54 with IBS, 43 CD, 42 ulcerative colitis) undergoing diagnostic ileocolonoscopy, who provided fecal samples.^8, Samples were analyzed with enzyme-linked immunosorbent assay. Patients with IBS had significantly higher levels of lactoferrin, calprotectin, and polymorphonuclear-elastase than patients who had ulcerative colitis or CD (all p<.001). In the ulcerative colitis and CD groups, there were higher levels of all 3 markers in patients who had inflammation compared with those who did not.

Clinically Useful

A test is clinically useful if the use of the results informs management decisions that improve the net health outcome of care. The net health outcome can be improved if patients receive correct therapy, more effective therapy, or avoid unnecessary therapy or testing.

Direct Evidence

Direct evidence of clinical utility is provided by studies that have compared health outcomes for patients managed with and without the test. Because these are intervention studies, the preferred evidence would be from randomized controlled trials (RCTs).

No randomized or comparative intervention studies supporting the clinical utility of fecal testing were identified.

Chain of Evidence

Indirect evidence of clinical utility rests on clinical validity. It is not possible to construct a chain of evidence because there is insufficient evidence of clinical validity to draw conclusions on clinical utility.

For individuals with gastrointestinal conditions such as suspected intestinal dysbiosis, irritable bowel syndrome (IBS), malabsorption, or small intestinal bacterial overgrowth who receive fecal analysis testing, the evidence includes several cohort and case-control studies comparing fecal microbiota in patients who had a known disease with healthy controls. The relevant outcomes are test validity, symptoms, and functional outcomes. The available retrospective cohort studies on fecal analysis have suggested that some components of the fecal microbiome and inflammatory markers may differ across patients with IBS subtypes. No studies were identified on the diagnostic accuracy of fecal analysis versus another diagnostic approach or that compared health outcomes in patients managed with and without fecal analysis tests. No studies were identified that directly informed the use of fecal analysis in the evaluation of intestinal dysbiosis, malabsorption, or small intestinal bacterial overgrowth. The evidence is insufficient to determine that the technology results in an improvement in the net health outcome.

Supplemental Information

The purpose of the following information is to provide reference material. Inclusion does not imply endorsement or alignment with the evidence review conclusions.

Practice Guidelines and Position Statements

Medicare National Coverage

There is no national coverage determination. In the absence of a national coverage determination, coverage decisions are left to the discretion of local Medicare carriers.

Ongoing and Unpublished Clinical Trials

Some currently ongoing and unpublished trials that might influence this review are listed in Table 2.

Table 3. Summary of Key Trials

References

Codes

Applicable Modifiers

As per correct coding guidelines

Policy History