Guidance for clinicians treating patients with FMT (Fecal Microbiota Transplants)

This short guide provides some general insight for clinicians who are treating patients with Fecal Microbiota Transplants (FMT), as far as what to expect and when to intervene. It should not be mistaken for medical advice.

It is written by Michael Harrop, a patient with a decade of experience and research. Michael has done countless FMTs from 12+ different donors. Michael also created and maintains HumanMicrobiome.info — see HumanMicrobiome.info/FMT for a deeper dive.

If clinicians encounter circumstances that are not covered by this guide you can reach out directly to Michael for consultation. But we cannot provide medical advice to patients.

Common symptoms & adverse events:

It's common for patients to feel feverish & chills, and possibly some initial diarrhea & other temporary side effects after the first 1-2 FMTs. It’s even possible for the patient’s overall condition to temporarily worsen. Often some of these symptoms can be a sign of a high-quality donor — symptoms of a "changing of the guard".

Generally, this should only last a couple of days before the patient begins to improve past their baseline. However, there are rare anecdotal reports of the initial worsening lasting much longer, and the patient then seeing significant improvements later on.

It is commonly recommended for people to push through adverse effects when it comes to diets, prebiotics, probiotics, and FMT. However, this is often just harmful advice and is often used to avoid blame for a bad donor, product, or intervention.

It can sometimes be difficult to tell whether something is a temporary side effect, or whether the donor is not good for the person. One of the ways we try to determine this is with our results tracking. If most people are improving from a donor then it’s more likely that an adverse event is only temporary. However, some patients only experience diarrhea or other unwanted symptoms and do not improve. Some patients also experience initial adverse effects, pause the treatment, and then resume and see benefits. Sometimes resuming with a smaller dose is what they found to be effective.

Often, FMT can change a patient’s ideal foods and medications. Medications that were helpful beforehand may no longer be needed, may start to cause problems, and may need to be reduced or stopped. For diet, a good practice is for patients to keep a detailed food & symptom diary and stick with a few basic foods they tolerate well, and then slowly try to add more in.

Antibiotics & poor outcomes:

Antibiotics are not supported prior to FMT, and may even be harmful: https://humanmicrobiome.info/fmt/#before-the-procedure

It’s also a bad idea to act too hastily to give a patient antibiotics after experiencing the common symptoms listed above. Antibiotics may undo and prevent the benefits of FMT. They should be saved for severe and life-threatening cases.

Antibiotics may be helpful to mitigate some poor outcomes after a bad FMT, but in general they usually only have temporary effects, often only as long as you keep taking them. It’s also not clear which antibiotic would be the best choice to mitigate a bad FMT outcome.

In general, the only remedy to a bad FMT outcome is another FMT from a better donor.

For our first two donors, neither was the best choice for everyone. Some people benefited more from one and less from the other. And some people even got worse from one and better from the other. And it’s not possible to predict which donor would be best for each person.

Even from the same donor, stool characteristics and effects can vary significantly. We consult donors about choosing only the best stools, but it’s ultimately up to their judgment. If someone has a bad result from one of our donors I would generally not recommend trying another stool from that same donor.