The Promise - and Perils - of Tinkering with our Bacteria

Jun 24, 2019

Colorized scanning electron micrograph of Escherichia coli, grown in culture and adhered to a cover slip.
Credit NAIAD/Attribution 2.0 Generic (CC BY 2.0)

The FDA has halted trials of fecal transplants after one recipient has died and another is ill. Both were being treated for an intestinal infection called C. difficile and received transplants from an ostensibly healthy donor who turned out to be carrying an antibiotic resistant strain of E. coli. The incident highlights the risks inherent in a procedure that has rapidly gained favor for treating a host of health problems.

Kjersti Aagaard, Henry and Emma Meyer chair of obstetrics and gynecology at Baylor College of Medicine, recently published an opinion piece in Nature Medicine in which she and Dr. Elizabeth Hohmann of Harvard University describe the need for caution and better regulation of fecal transplants. But Aagaard says she was still a bit surprised by news of the death.

“While we urged exercising caution, I think that none of us imagined that death was ultimately in the profile,” Aagaard said.

Research in the past few years has shown that the suite of bacteria that lives on and in us – collectively known as our microbiome – can influence our health in myriad ways. In particular, our gut microbes have been linked to obesity, chemotherapy sensitivity, infertility, depression, and more.

The fact that some microbial collections confer health benefits while others carry risks led to the idea of swapping microbiomes. And fecal transplantation is a way of doing that, albeit a crude one, Aagaard says.

“We're quite literally taking the complete microbial ecology from one human volunteer and putting it into another,” explained Aagaard. “That's like taking a landscape with all of its niches, and valleys, and mountains, and lakes, and moving it to a whole other site. What is retained within that complex ecological landscape we don't entirely know.”

The FDA has called for more comprehensive screening of fecal transplant donors, but Aagard says that won’t eliminate the risks.

“We can widen the scope of what we screen for - things that we know are dangerous,” Aagaard said. “But then there's the things we don't really know how and what to screen for, and those may be equally - if not greater - problematic over time.”

For example, there’s no way to know whether a donor might, at some point in the future, develop cancer or a mental health disorder that could be linked back to their microbiome, or whether that risk would be transferred to the recipient.

Aagard says it’s incumbent on researchers and doctors to explain to patients not only the potential benefits of microbial manipulations, but also the possible risks, and – importantly – what we still don’t know.

“The folks that we need to bring into this discussion are patients and the public, at large,” Aagaard said. “What measure of risk are people willing to incur in order to have a disease trajectory reversed?”

Aagaard doesn’t see any of this as a reason to stop research on what could prove to be incredibly powerful medical interventions. She envisions eventually being able to give patients specific, lab-grown bacterial strains and create treatments that are more tailored and reversible than current medications.

“The reality of making this all come to fruition is going to require a lot more research,” she said. “But it needs to be carefully regulated, carefully controlled, carefully explained, and very carefully thought through.”