Fig. 1. Fecal microbiota transplantation (FMT) aims to restore a healthy gut microbiota.

a In an initial healthy gut, the microbial community typically contains many different taxa and displays very high taxonomic and functional diversity. Most of those taxa are benign. Some of them can even keep out opportunistic pathogens such as C. difficile. b Antibiotic administration leads to low taxonomic diversity and to a disrupted gut microbiota, which allows colonization by C. difficile. c C. difficile spores are typically ingested following contact with contaminated biotic or abiotic surfaces, then germinate in the gut to a vegetative cell-type and produce potent gut-damaging toxins during a late growth stage. This leads the development of C. difficile infection (CDI). Ironically, standard treatment of CDI generally involves prescription of antibiotics such as metronidazole or vancomycin. Those antibiotics kill C. difficile but spores can remain in the gut, rendering recurrent CDI (rCDI). d Transplanting the fecal material from a healthy donor to the patient’s gut can restore the healthy gut microbiota.