Find policies, billing codes, payers, states, and providers
Fecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing
Customize your policy alerts
Sign up for all Oscar Health policy alerts
Know when Oscar Health releases new policies or updates existing guidance.
Monitor payer policy activity
Criteria for laboratory analysis of donor stool prior to fecal microbiota transplant (FMT) and coverage stance on fecal analysis tests proposed for diagnosing intestinal dysbiosis; applies to Oscar Health claims and providers seeking reimbursement guidance.
No material clinical or coverage changes in this revision.
Coverage Determinations and Criteria
FMT donor screening and fecal analysis coverage
Covered prior to donation for FMT when the listed stool tests are performed by culture or NAAT; NAAT for certain organisms is explicitly not acceptable for donor screening.
List from policy III.1
List from policy III.2
List from policy III.3
List from policy III.4
Diagnostic stool testing indications
Covered when used to exclude infectious causes or assess intestinal inflammation in patients with diarrhea or when evaluating suspected IBD.
Sources: WGO, ECCO/ESGAR, BSG
FMT consideration for C. difficile infection
Covered when recurrence criteria and prior standard-of-care antibiotic therapy have been met.
Sources: AGA, ACG
Tests specifically listed in this policy as DOES NOT MEET CRITERIA are not supported for coverage because there is a lack of published scientific literature demonstrating that these tests are required and beneficial for diagnosis or treatment. Providers should not expect coverage for donor stool NAATs or fecal analyses designated as not meeting criteria unless new, high-quality evidence supporting clinical utility is available.
Fecal microbiota transplantation (FMT) is not recommended for treatment of functional gastrointestinal symptoms, global irritable bowel syndrome (IBS), ulcerative colitis, Crohn’s disease, or pouchitis outside of a clinical trial setting. Professional society guidance cited in this policy advises that FMT for inflammatory bowel disease remains investigational except when IBD is complicated by recurrent Clostridioides difficile infection.
The FDA has issued safety communications highlighting the risk of serious adverse events likely due to transmission of pathogenic organisms with fecal microbiota transplantation. Failure to meet recommended donor screening and testing protocols described in this policy may therefore justify exclusion of donor material or denial of coverage for FMT-related services.
The fecal analysis components enumerated in section III.4 of this policy (for example, triglycerides; chymotrypsin; various short-chain and long-chain fatty acids; quantification of specific bacterial genera and 'potential pathogens'; fecal yeast identification; beta‑glucuronidase; pH; fecal secretory IgA, among others) are considered to NOT MEET CRITERIA when proposed as diagnostic tests for intestinal dysbiosis, IBS, malabsorption, or small intestinal bacterial overgrowth due to insufficient evidence of clinical utility.
For patients who meet diagnostic criteria for IBS, certain stool tests are unnecessary to confirm the diagnosis. Examples specifically noted in guideline sources and reflected in this policy include faecal ova and parasite testing and faecal occult blood, which are listed among tests that are not required to establish an IBS diagnosis.
Procedure Codes and Billing
| 82542 | Column chromatography, includes mass spectrometry, non-drug analyte(s) not elsewhere specified, qualitative or quantitative, each specimen. |
| 82705 | Fat or lipids, feces; qualitative. |
| 82710 | Fat or lipids, feces; quantitative. |
| 82715 | Fat differential, feces, quantitative. |
| 83986 | pH; body fluid, not otherwise specified. |
| 84311 | Spectrophotometry, analyte not elsewhere specified. |
| 87045 | Culture, bacterial; stool, aerobic, with isolation and preliminary examination, Salmonella and Shigella species. |
| 87046 | Culture, bacterial; stool, aerobic, additional pathogens, isolation and presumptive identification of isolates, each plate. |
| 87075 | Culture, bacterial; any source, except blood, anaerobic with isolation and presumptive identification of isolates. |
| 87076 | Culture, bacterial; anaerobic isolate, additional methods required for definitive identification, each isolate. |
Provider Responsibilities, Authorization, and Documentation
Authorization and medical necessity required
Services must meet authorization and medical necessity guidelines; coverage does not guarantee reimbursement and is dependent on the member's benefit coverage at the time of request. Providers are responsible for submission of accurate documentation of services performed and claims may be denied or recouped if coding/billing guidelines or current reimbursement policies are not followed.
- Verify member benefits and obtain prior authorization when required.
- Ensure medical necessity is documented in the request to support approval.
Procedure codes may require authorization
Certain fecal laboratory and culture procedure codes listed in the policy may be subject to authorization per payer rules; providers must document medical necessity consistent with applicable guidelines when submitting claims for these codes.
Prior authorization expectations for FMT
When seeking approval for FMT-related services, follow professional-society guidance and FDA safety communications and document the indication, prior treatments, and donor screening steps as part of the authorization request.
- Document prior standard-of-care therapies and the clinical indication for FMT.
- Include evidence of adherence to society guidelines and relevant FDA safety communications in the prior authorization submission.
Donor screening steps
Donor screening for FMT must include evaluation of donor history, serum testing, and stool testing prior to transplantation; document these screening steps in the medical record.
- Capture donor medical history and risk assessment.
- Record results of required serum and stool laboratory assays before use of donor stool.
FMT after antibiotics for recurrent CDI
For recurrent C. difficile infection, consider FMT after completion of standard-of-care antibiotics (for example, after a second recurrence); document prior antibiotic therapy and clinical course when requesting FMT.
- Confirm completion of recommended antibiotic regimens prior to FMT consideration.
- Document recurrence number and any high-risk features cited by guideline recommendations.
Provider documentation and donor records may be required
Follow all documentation and coding requirements outlined in the policy and submit supporting records as requested; include donor records when applicable to support medical necessity and safety of FMT.
- Provide accurate CPT/HCPCS/ICD-10 coding and clinical documentation for services performed.
- Include donor history and test results in records when reimbursement for FMT-related services is sought.
Required documentation
Providers must submit accurate documentation of services performed, including appropriate coding per CPT/HCPCS/ICD-10, and may need to provide donor history, serum testing, and stool testing documentation for FMT.
- Ensure clinical notes and test reports supporting medical necessity are included with prior authorization requests or claim submissions.
Donor screening and quarantine
Donors should complete a health questionnaire and laboratory screening assays both before and after donation; stool samples may be quarantined until post-donation MDRO tests are confirmed negative (bookend testing within 60 days is acceptable).
- Maintain donor questionnaire and both pre- and post-donation laboratory results in donor records.
- Quarantine donated stool until post-donation MDRO testing confirms negative results (bookend testing no more than 60 days apart).
Document donor screening and testing per FDA/society guidance
Document adherence to FDA and society guidance on donor screening and stool testing for FMT, including screening for transmissible pathogens and following updated COVID-19 related protections.
- Record specific tests performed to meet FDA/BSG recommendations (including MDRO testing).
- Include COVID-19–related donor screening or testing performed per FDA updates.
Coding and documentation risk
Claims may be denied or recouped if coding/billing guidelines or current reimbursement policies are not followed and documentation is not accurate; submit complete and correct coding and supporting clinical documentation to reduce risk of denial.
- Follow industry-standard coding guidelines and payer-specific rules when billing for fecal testing or FMT.
- Retain and provide requested documentation promptly if a claim is audited.
Donor MDRO exclusion
Donor stool that tests positive for MDROs (for example ESBL-producing Enterobacteriaceae, VRE, CRE, MRSA) should not be used for FMT and its use would trigger exclusion of that donor stool from transplantation.
- Do not use donors or stool samples that test positive for the MDROs specified by FDA/BSG guidance.
- Document MDRO test results and exclude positive donors from the donor pool.
FDA safety communication implications
FDA safety communications about transmission risks of multi-drug resistant organisms and other pathogenic organisms in FMT affect coverage and safety practices; failure to meet FDA-recommended donor screening/testing requirements may provide grounds for claim denial.
- Incorporate FDA safety recommendations into donor screening and testing protocols.
- Retain documentation showing compliance with FDA safety communications to support authorization and claims.
Background and Scope
Intestinal dysbiosis refers to an imbalance in the composition, diversity, or metabolic function of the gut microbiome that has been associated with conditions such as IBS, inflammatory bowel disease, celiac disease, and metabolic disorders. Proposed direct (microbial composition) and indirect (metabolite or enzyme) fecal assays have not established standardized normal ranges or demonstrated consistent clinical benefit, limiting their role in routine care. Fecal microbiota transplantation (FMT) is an intervention intended to restore microbial community structure but requires rigorous donor screening (including targeted culture and NAAT panels described in this policy) to mitigate infectious risks and align with professional-society and regulatory safety guidance.
Key Terms and Definitions
OpenPayer is powered by Trek Health's payer performance platform. Trek continuously ingests, validates, and normalizes Transparency in Coverage data alongside payer policies and other commercial payer data to create a structured payer intelligence foundation. OpenPayer uses this foundation to deliver personalized search results, dynamically generated policy pages, and tailored policy monitoring based on each user's payers, specialties, billing codes, and areas of interest. The same intelligence powers broader payer performance workflows, including reimbursement benchmarking, contract evaluation, payer negotiations, and financial decision-making.