Fecal microbiota transplants (FMT), once heralded as a miracle fix for gut-related diseases, may come with unintended consequences, according to new research from the University of Chicago published in Cell.
While FMT is FDA-approved only for recurrent C. difficile infections, it’s increasingly being explored for conditions like IBD, obesity, diabetes, and even autism. But researchers led by Dr. Eugene Chang and Dr. Orlando DeLeon warn that transplanting microbes from the colon into other gut regions—like the small intestine—can result in mismatched colonization, metabolic shifts, and even behavioral changes.
The study found that these “regional mismatches” persist for months and may permanently alter the gut environment, reshaping tissue identity in ways that benefit transplanted microbes at the host’s expense. Researchers call for a move toward “omni-microbial transplants” that account for the gut’s distinct microbial zones, rather than a one-size-fits-all approach.