April 30, 2017

Frozen stool for FMT: Is it safe and effective?

Here is another letter to me about


I saved some stool samples (prepped fecal slurry) prior to antibiotic use for an autologous/self fecal transplantation. The samples have been frozen at -20 (home deep freezer) for just over 3 months time. I would still like to utilize them, but have  not been able to find any information on whether or not the samples would still be safe to use. I would assume that any shift in the microbiota composition would have happened early on and is now stable… and that it would still be preferable to finding a donor in order to obtain fresh. I am hesitant without hearing from someone who may have more information regarding the safety. I’d appreciate any insight. I had surgery and was taking narcotics as well as IV antibiotics in the hospital. The samples remained frozen for this long because of several weeks on medication. I have been taking probiotics both during and after medication use (Digesta Flora by Perque and HMF with FOS) as well as S. boulardii. The digestive disruption is mild to moderate at this point, but I do have a history of IBS, which resolved after several years of a whole foods, grain-free diet as well as lifestyle changes. Because I have read so much about the loss of microbiotic diversity after antibiotic and medication usage, I wanted to inoculate myself with my own bacteria and that is why I saved it. I heard about it from my naturopath, but she was not sure if I should still use the samples after this length of time.

Thank you,


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Hi J,

Frozen stool would still be safe to use and most of the bacteria would still be active once warmed to body temperature and no more decomposition should have occurred after it was frozen.  Some of the doctors who spoke at the human microbiome conference in July 2013 said they used frozen slurry mixed from donors to administer fecal transplants.
 You are are right that this would be better than using stool from another person both in terms of safety and general compatibility with your body. Anti-biotics have long been known to cause diarrhea and studies now indicate that there are likely to be permanent alterations in gut flora after the antibiotics are stopped. Knowing this many years ago a researcher at Stanford used fecal transplants to resolve anti-biotic induced diarrhea in surgery patients back in the 1950s. While there were some different medical standards at the time, the impact of antibiotics and the benefits of restoring the gut bacteria was considered and anecdotal evidence of its success appeared to be favorable.
So using your own stool either through capsules or through enemas, depending on how much of this stool you have could be very beneficial to digestive function. Having a restored microbiota could potentially lower lower any risk you could have of infectious colitis such as colitis related to c. diff bacteria.
I would recommend stopping the pro-biotic supplements while you are doing the fecal transplants using your own stool to restore you pre-surgery microbiome and stop taking the other pro-biotics for a good period of time afterwards to give it a chance to re establish itself without anything else interfering with it and measure the results. I don’t think even a high quality pro-biotic supplement which would most likely include no more than a dozen strains of bacteria at most can bring about better and more sustainable long-term results than simply establishing a complete and healthy microbiome from your own healthy stool which includes potentially hundreds of different strains of bacteria.