This New Personal Poop Banking Service Lets You Save Your Microbiome For A Rainy Day

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This New Personal Poop Banking Service Lets You Save Your Microbiome For A Rainy Day
[Illustration: lynea via Shutterstock]

Nowadays when you take a course of antibiotics, many doctors will recommend eating a lot of yogurt or popping some probiotics to restore the good bacteria that the drugs wipe out. But how well does that work? One recent study found it can take up to a full year for the gut’s microbial ecosystem to recover from a single antibiotic course.


Totally reviving your gut’s microbial ecosystem to its healthy state is hard to do on probiotics alone. Probiotic foods or pills offer only a small drop in the bucket compared to the vast trillions of diverse microorganisms that live in your digestive tract.

In the future, patients may turn to a more direct remedy: saving, or “banking,” their healthy microbiome via their own feces and transplanting it back later when it’s needed.

“Ultimately, you can imagine patients chasing their standard antibiotics with a microbiome pill to repopulate their gut,” says James Burgess, co-founder and executive director of a nonprofit called OpenBiome.

It may sound a little unappetizing, but it’s already happening. OpenBiome is pioneering this process, albeit for a more limited set of circumstances. In the last few years, with the FDA’s tacit approval, doctors have successfully used microbiome transplants (often called fecal matter transplants or FMTs) to cure otherwise untreatable infections of an antibiotic-resistant bacteria called C.diff. In more than 90% of cases, repopulating patients’ guts with a donor’s healthy microbiome had cured them–even after all drugs failed.

Many of these transplants, which now only require swallowing a pill, have been done with OpenBiome’s material. The group serves as a repository and screening facility for willing “poop donors” and has provided safe transplant material to 7,000 patients. Now, it is piloting a new service called PersonalBiome, which will allow people who are vulnerable to C. diff infections to proactively save their own microbiome for a rainy day. Burgess compares it to the way a woman might freeze her eggs, if she’s worried about her future fertility.

Right now, PersonalBiome’s services are limited to those who are at risk of recurrent C. diff, which include people who have had it before. But as regulations evolve, Burgess believes microbiome banking could soon be useful for people at risk to other kinds of deadly antibiotic-resistant infections. A study in mice, for example, has shown that deadly drug resistant bacteria like VRE could also respond well to fecal transplants. Cancer patients and others with suppressed immune systems could also be early beneficiaries. New York’s Memorial Sloan Kettering Hospital is already doing trials that have shown leukemia patients with diverse microbiomes have higher survival after surgery than those who do not–the head investigator, Eric Pamer, is experimenting with proactive microbiome banking.


“Our big picture is to roll this out to these high-risk patient populations who develop a lot of these health care associated infections,” says Burgess.

PersonalBiome seems to be the only service offering microbiome banking for now. The startup uBiome does offer to save the genetic information in your microbiome (after you swab your toilet paper and send a sample to them), but doesn’t save the actual material. “The idea is that if your microbiome changes over time, you can store it now, then two years from now you’ll know how it’s different,” uBiome founder Jessica Richman says.

In general, researchers suspect our microbiomes may play a larger role in determining our health than anyone realized until recently. Our gut flora may be linked to conditions ranging from asthma to obesity to autism, studies have found. Yet there are many questions to answer about how changing our microbiomes could improve our health. And as for transplants after our microbiomes are depleted? There are still many safety questions to answer about how microbiome banking would work and the true scope of its potential.

Even the FDA still considers transplanting one’s own microbiome as subject to federal regulatory approval. But Burgess says a self-transplant is generally considered safer and likely healthier than relying on donors. In theory, the agency could one day make it easier to bank and transplant one’s own microbiome, as it has done with umbilical cord blood.

Whether PersonalBiome is a service that will one day be useful to everyone, even perfectly healthy people, isn’t yet clear. For now, to participate in the pilot phase, you’ll have to stop by their laboratory in Medford, Massachusetts. Eventually, they hope to conduct banking by mail, so it can be more available to anyone.

About the author

Jessica Leber is a staff editor and writer for Fast Company's Co.Exist. Previously, she was a business reporter for MIT’s Technology Review and an environmental reporter at ClimateWire.