This year The PediaBlog has explored the microbiome (here, here, and here), made up of trillions of bacteria in our bodies living in symbiosis with each human cell, and affecting the health of each of us individually, as well as all of us communally. Moises Velasquez-Manoff wonders whether one’s own (presumably healthy) feces, full of intestinal bacteria, could some day be used as medication in times of need, such as after a course of antibiotics for bacterial infections, during courses of chemotherapy for cancer, or prior to stem cell transplants (when a cocktail of antibiotics and chemotherapeutic drugs purposely obliterate the microbial members of the microbiome):

By last August, my 1-year-old son had taken five courses of antibiotics for recurrent ear infections. That was alarming. By age 10, the average American child has had about 10 courses, and some microbiologists argue that even one course a year is too many — that it might damage our native microbial ecosystem, with far-reaching consequences.

My son was off to a worrisome start. Why, I wondered, didn’t doctors work harder to prevent this collateral damage, not with store-bought probiotics, but with “microbial restoration”? Why didn’t we reinfuse patients with their own microbes after antibiotics?

The scientific term for this is “autologous fecal transplant.” In theory, it could work like a system reboot disk works for your computer. You’d freeze your feces, which are roughly half microbes, and when your microbiome became corrupted or was depleted with antimicrobials, you could “reinstall” it from a backup copy.


The “fecal transplant” concept isn’t new. Velasquez-Manoff says the technique was successfully tried sixty years ago and that today, it is an effective treatment for Clostridium difficile (“C. diff”) colitis. The idea of “banking stool” — collecting, freezing, and saving one’s healthy microbiome for a time of need — is starting to take hold in medical facilities around the country. For children, stool banking and fecal transplantation may not be as simple a proposition as it is with adults. For instance, Velasquez-Manoff’s son got ear tubes to prevent the need for more antibiotics but not a fecal transplant:

I didn’t give my son a self-transplant. The approach is unproven, and anyway, I hadn’t stored any of his microbes from his pre-antibiotic days. Even if I had, as the Stanford microbiologists Justin and Erica Sonnenburg reminded me, self-transplants aren’t as straightforward for children as they are for adults. The infant microbiota changes from month to month, moving erratically toward an adultlike state. If I were to store microbes from month six, and reintroduce them at month 12, the microbial community might no longer be appropriate for that stage of development.

But clearly, this idea needs testing. It may be one way to prevent infections and some percentage of lifelong, chronic diseases, not with fancy drugs or expensive procedures, but simply by restoring, after antimicrobial disturbances, the microbes we already carry.