OpenBiome was founded to make offering FMT easier, safer, and less expensive for clinicians. Here, you'll find clinical guidance to assist you at every stage of the process, from delivery modality selection to patient follow-up.

Our Clinical Outreach Team is available 9 AM - 5 PM, Monday - Friday to answer and questions you might have at any stage. Write to them at or call 617-575-2201, option 3.

    • Fecal material can be administered either through the lower gastrointestinal tract (e.g. by colonoscope/sigmoidoscope or enema) through the upper gastrointestinal tract (e.g. by nasogastric/nasoduodenal tube), or by orally administered capsules, and OpenBiome provides microbiota preparations for each of these options. Each route of administration carries unique risks and benefits, so it is important to select the appropriate mode of delivery for your patient's health condition.
    • Informed consent: Obtaining informed consent is a mandatory and crucial step in preparing patients for FMT, which is regulated by the FDA as an investigational procedure. Informed consent is defined as the process through which physicians share relevant information with patients in a language that is understandable to them and provide patients with sufficient time to consider their treatment options. Patients undergoing FMT should recognize that FMT is an investigational procedure that is permitted but not approved by the FDA to treat recurrent C. difficile. They should also understand both the procedural and microbiota transference-related risks including transmission of multidrug-resistant organisms. Finally, physicians and patients should discuss alternative treatment options such as long-term vancomycin therapy, surgery, and no treatment at all.

      If needed, a template for obtaining informed consent can be requested at You may also find our Pre-FMT Patient Guide a helpful educational resource.

      48 hours before treatment: While evidence is limited, standard practice includes discontinuation of anti-C. difficile antibiotics two days before FMT. This will ensure that antibiotics do not impact the newly transferred microbiota. Some groups recommend a standard large volume bowel lavage for all modes of delivery; however, anecdotal evidence suggests that limited or no preparation may be equally effective. For upper and oral delivery (excluding capsule delivery), it is recommended to administer a proton pump inhibitor the evening before and morning of FMT. This will minimize the impact of gastric acid on the donor microbiota during the procedure.
    • Thawing: OpenBiome's microbiota preparations for upper or lower delivery should be thawed 1-4 hours prior to the procedure, according to the instructions for thawing included with each shipment. OpenBiome's FMT Capsule DE do not require thawing, and should be kept frozen until immediately prior to administration. For more information, please see our Storage Controls & Material Specifications.

      OpenBiome material can be pre-loaded directly from the OpenBiome container using standard syringes. Alternatively, microbiota preparations can be transferred to a sterile container, such as a clean K-basin, prior to loading syringes.

    • Upper Delivery

      For OpenBiome material, a 30 mL Upper Delivery microbiota preparation should be used for all forms of upper delivery. This is a formulation specifically prepared to ensure appropriate concentration for upper delivery. Use of the less concentrated 250 mL Lower Delivery microbiota preparation for delivery by an upper GI route of administration can result in aspiration of fecal material and is not recommended. If using a naso-enteric tube, tube placement should be confirmed by radiogaph or fluoroscopy before fecal installation. Endoscopic delivery should be performed under direct visualization. Material should then be directly delivered through the naso-enteric tube or endoscope.

      Lower Delivery: Colonoscopy or Sigmoidoscopy

      For OpenBiome material, a 250 mL Lower Delivery microbiota preparation should be used for all forms of lower delivery, most commonly performed by colonoscopy. Sigmoidoscopy has also been successfully used for patients who are unable to tolerate a full colonoscopy. Anecdotal recommendations suggest infusion of all material in the cecum or most proximal aspect safely reached.

      Lower Delivery: Retention Enema

      Retention enema is generally less effective than upper delivery or colonoscopy. However, retention enema may be best option for patients with co-morbidities that may increase the risks associated with other administration routes. Transfer of all 250 mL of the microbiota preparation to a standard retention enema bag is recommended. Data is limited on timing parameters, but evidence suggests that material should be administered over 1 hour and retained for 1 hour. Enema delivery may require multiple treatments, particularly in an elderly population with poor rectal sphincter tone. Effort should be made to periodically rotate the patient from LLD, to supine, to RLD.

      Oral Delivery: FMT Capsule DE

      Capsules can serve as a less invasive alternative to naso-enteric and lower routes of FMT administration. For full guidance on administration of FMT Capsule DE, please see the FMT Capsule DE Clinical Primer.

    • It is paramount to follow up with patients to monitor for adverse events and evaluate whether resolution of C. difficile has occurred. Standard clinical practices suggests a clinic visit 8 weeks post-FMT for assessment.

      Certain symptoms such as changes in bowel habits, abdominal pain, bloating and cramping are common after FMT, but these side effects are transient. Patients should be instructed about when to seek medical attention for potential adverse events. Additionally, patients should receive educational material on ways to reduce the risk of C. difficile re-infection. OpenBiome's Post-FMT Patient Guide provides helpful guidance about future antibiotic use.