Donations for FMT await use in a deep freeze. (OpenBiome)

You know what's great? Fecal Microbiota Transplants. But while FMT — yes, literally the transplantation of one person's poo into another person's body — has already saved lives, the cutting-edge therapy is still only approved for treating one condition, and even then it doesn't always work. As part of a special issue on the bacteria that live in our guts, Science has just published a new study that takes a closer look at how FMT affects patients. The study, led by the European Molecular Biology Laboratory, suggests that more personalized donor selection may be the key to better FMT.

FMT is arguably the most successful effort to hack the microbes that live in and around us (known as our microbiome or microbiota) to date. The treatment is used to treat chronic infections of the bacteria Clostridium difficileThese infections can cause crippling and even fatal gastrointestinal problems, and are often resistant to antibiotics. When a patient's gut is seeded with microbes from healthy donors (by way of poop, naturally) the bad bugs are often outcompeted by better bacteria.

There are now companies that screen potential donors — the selection process is rigorous — and pay them handsomely for their precious poo. Researchers around the world have worked to make the treatment both more practical and more palatable: Studies have shown that frozen donations are as good as fresh, which means that donation centers can freeze, test, store  and ship their microbial slurries across the country. Other studies have tested benign, frozen oral pills as a delivery method, providing a painless alternative to the traditional practice of using nasal or rectal tubes to transplant the donation.

But many hope that FMT can have a broader reach one day. It seems increasingly clear that humans have an intricate, incredibly important relationship with the microbes that live inside them. Scientists are still working on figuring out what a truly ideal gut microbiome looks like — or if there even is one — but as they link more microbes to health or illness, FMT becomes an ever more attractive way of replacing "bad" bacteria with "good." Other bowel diseases like colitis are likely next on the FMT success list, but it wouldn't be crazy to cross your fingers for a weight loss aid that came straight from someone else's bowels.

"Ultimately, the goal is to move from a stool transplant to something more manageable, such as a pill," first author Simone Li said in a statement. "Our work shows that this is likely going to be a personalized bacterial cocktail, rather than a one-size-fits-all solution."

Li and her colleagues came to that conclusion by examining bacteria from 5 FMT patients before and after their treatment, as well as studying the stool from their donors and 5 patients receiving a placebo. And they didn't just look at species of bacteria, but at the different strains, or subtypes, that those bacteria came in. Many species of bacteria — E. coli, for example — have some strains that are perfectly safe and others that can be dangerous.

"Until now, we could only look at what species of microbe establish themselves in (or disappear from) a patient’s gut after FMT, but we couldn’t draw any conclusions about species that a patient had before and after the transplant: We had no way of knowing if those microbes were still the patient’s, or if they came from the donor," Peer Bork, who co-led the research with Shinichi Sunagawa, told The Post in an email. "Now that we can track strains, we can make that distinction."

The researchers were surprised to find that many patients maintained their own strains of bacteria even as related donor strains set up shop. In all but one of the patients they studied, about 50 percent of donor bacteria that shared a species (but not strain) with native bugs were still cohabiting with their cousins three months later.

They also found that donated bacteria were much more likely to stick around if another member of their species was already in the recipient's gut, possibly because the recipient's immune system is less likely to flag them as foreign invaders.

The big takeaway, Bork explained, is that we have a lot to learn about what actually goes on when we transplant poo — and that there's no such thing as a perfect poo donor. While good health is important — adding new pathogens to the gut of a C. diff patient would be disastrous — the best donor might depend on the patient.

"There is no super donor, but important is a kind of donor-recipient 'compatibility,' " Bork wrote, "again suggesting more personalized approaches."

Correction: A previous version of this post referred to 55 patients, when in fact the researchers took 55 samples from 10 patients. 

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