Medical Policy

Subject:Fecal Analysis in the Diagnosis of Intestinal Dysbiosis
Policy #:  LAB.00016Current Effective Date:  10/14/2014
Status:ReviewedLast Review Date:  08/14/2014


This document addresses the use of fecal analysis for the diagnosis of intestinal dysbiosis, which has been defined as a state of disordered microbial ecology that causes disease.  Evaluation of intestinal dysbiosis may be suggested for people with gastrointestinal symptoms such as indigestion, constipation, diarrhea, gas, bloating or abdominal pain.  Many of these symptoms overlap with other gastrointestinal disorders such as irritable bowel, malabsorption or small intestinal overgrowth of bacteria.

Position Statement

Investigational and Not Medically Necessary:

Fecal analysis of the following components is considered investigational and not medically necessary as a diagnostic test for the evaluation of intestinal dysbiosis, irritable bowel syndrome, malabsorption or small intestinal overgrowth of bacteria:


While the literature includes much discussion regarding the relationship between intestinal microflora and various disorders, intestinal dysbiosis as a specific disorder is poorly defined.  A literature search revealed no published studies establishing diagnostic criteria for this disorder.  The gastrointestinal symptoms attributed to intestinal dysbiosis (i.e., bloating, flatulence, diarrhea or constipation) overlap in part with either irritable bowel syndrome or small intestinal bacterial overgrowth syndrome.  The diagnosis of irritable bowel syndrome is typically made clinically, based on a set of criteria referred to as the "Rome" criteria.  Small intestine bacterial overgrowth may result from altered motility (including blind loops), decreased intestinal acidity, exposure to antibiotics, or surgical resection of the small bowel.  Symptoms include malabsorption, diarrhea, fatigue and lethargy.  Although the diagnosis of bacterial overgrowth may be made clinically and the condition treated empirically with antibiotics, the laboratory gold standard for diagnosis consists of culture of a jejunal fluid sample.  Recently hydrogen breath tests, commonly used to evaluate lactose intolerance, have been adapted for use in diagnosing both small intestinal bacteria overgrowth and irritable bowel disease.  No studies in the published literature were identified that described analysis of a stool sample bacterial flora or metabolic products as a diagnostic technique for irritable bowel syndrome or small intestine bacterial overgrowth.

Measurement of fecal fat (i.e., qualitative, quantitative and fat differential) is an established diagnostic technique for malabsorption.  In contrast, a literature search did not identify any published studies regarding the diagnostic performance of fecal analysis of digestion, absorption, microbiology, metabolic markers or immunology as a diagnostic tool for suspected malabsorption syndrome, small intestine bacterial overgrowth or intestinal dysbiosis.  Chronic intestinal candidiasis has been linked with various gastrointestinal complaints as well as systemic complaints, such as chronic fatigue syndrome.  However, similar to intestinal dysbiosis, chronic intestinal candidiasis is an ill-defined condition without established diagnostic parameters.

Finally, there have not been any studies published to date linking fecal testing for dysbiosis with any specific treatment or successful health outcomes post-treatment.  Further investigation is warranted.


The symptoms and conditions that have been attributed to dysbiosis include chronic intestinal disorders including irritable bowel disease, inflammatory or autoimmune disorders, food allergy, atopic eczema, unexplained fatigue, arthritis and ankylosing spondylitis, malnutrition or neuropsychiatric symptoms, including autism, and breast and colon cancer.

Laboratory analysis of both stool and urine has been investigated as markers of dysbiosis.  Reference laboratories specializing in the evaluation of dysbiosis may offer comprehensive testing of various aspects of digestion, absorption, microbiology and metabolic markers.  For example, Genova Diagnostics offers a "Comprehensive Digestive Stool Analysis" that evaluates a stool sample for the following components:




Metabolic Markers


Results are reported both individually, or combined into a "dysbiosis risk index," which is based upon gut microbiology, pH and short chain fatty acids.


Autoimmune: An overactive response of the body against substances and tissues that are normally not recognized as a threat by the body.

Intestinal flora: Harmless microorganisms (e.g., bacteria) that inhabit the intestinal tract and are essential for its normal functioning.


The following codes for treatments and procedures applicable to this document are included below for informational purposes. Inclusion or exclusion of a procedure, diagnosis or device code(s) does not constitute or imply member coverage or provider reimbursement policy. Please refer to the member's contract benefits in effect at the time of service to determine coverage or non-coverage of these services as it applies to an individual member.

When Services are Investigational and Not Medically Necessary:
When the code(s) describes a procedure indicated in the Position Statement section as investigational and not medically necessary.

89240Unlisted miscellaneous pathology test [when specified as fecal analysis for intestinal dysbiosis]
ICD-9 Diagnosis[For dates of service prior to 10/01/2015]
 All diagnoses, including but not limited to the following:
564.1Irritable bowel syndrome
569.9Unspecified disorder of intestine [no specific diagnosis code for intestinal dysbiosis]
ICD-10 Diagnosis[For dates of service on or after 10/01/2015]
 All diagnoses, including but not limited to the following:
K58.0-K58.9Irritable bowel syndrome
K63.9Disease of intestine, unspecified (no specific diagnosis code for intestinal dysbiosis)

Peer Reviewed Publications:

  1. Pimentel M, Chow EJ, Lin HC.  Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am J Gastroenterol. 2000; 95(12):3503-3506.
  2. Vanner SJ, Depew WT, Paterson WG, et al.  Predictive value of the Rome criteria for diagnosing the irritable bowel syndrome.  Am J Gastroenterol. 1999; 94(10):2912-2917.

 Government Agency, Medical Society, and Other Authoritative Publications:

  1. American Gastroenterological Association (AGA).  Medical position statement: irritable bowel syndrome. Gastroenterology. 2002; 123(6):2105-2107.

Fecal Analysis in the Diagnosis of Intestinal Dysbiosis
Genova Diagnostics
GI Effects Comprehensive Profile
Intestinal Dysbiosis

Document History
Reviewed08/14/2014Medical Policy & Technology Assessment Committee (MPTAC) review.  No change to position statement. Updated Description/Scope and Coding sections.
Reviewed08/08/2013MPTAC review.  No changes to position statement.
Reviewed08/09/2012MPTAC review.  No changes to position statement.
Reviewed08/18/2011MPTAC review.  No changes to position statement.
Reviewed08/19/2010MPTAC review.  No changes to position statement.
Reviewed08/27/2009MPTAC review.  No changes to position statement.
Reviewed08/28/2008MPTAC review. No changes to position statement.
 02/21/2008The phrase "investigational/not medically necessary" was clarified to read "investigational and not medically necessary." This change was approved at the November 29, 2007 MPTAC meeting.
Reviewed08/23/2007MPTAC review. No changes to position statement.
Reviewed09/14/2006MPTAC review.  No changes to position statement.
 11/17/2005Added reference for Centers for Medicare and Medicaid Services (CMS) – National Coverage Determination (NCD).
Revised09/22/2005MPTAC review.  Revision based on Pre-merger Anthem and Pre-merger WellPoint Harmonization. 
Pre-Merger Organizations

Last Review Date

Document Number


Anthem, Inc.


WellPoint Health Networks, Inc.


2.01.21Fecal Analysis in the Diagnosis of Intestinal Dysbiosis