Clostridium (
Clostridioides) difficile infection (CDI) is associated with
dysbiosis. C. difficile has a characteristic propensity to persist and recur 1 to 4 weeks
after treatment, but the mechanism is unknown. We hypothesized that C. difficile may persist by manipulating the intestinal microenvironment, thereby hampering gut microbiota reconstitution following
antibiotic-mediated
dysbiosis. By screening stools from CDI patients for unique markers, a metabolite identified to be
indole by mass spectrometry and Fourier transform infrared spectroscopy was identified. The average fecal
indole concentration detected in CDI patients (n = 216; mean, 1,684.0 ± 84.4 µM) was significantly higher than in stools of patients with non-C. difficile
diarrhea (n = 204; mean, 762.8 ± 53.8 µM). Certain intestinal bacteria, but not C. difficile, produce
indole, a potent antimicrobial
antioxidant. Remarkably, C. difficile induced other
indole-producing gut microbes to produce increasing amounts of
indole. Furthermore, a C. difficile accessory gene regulator 1 quorum sensing system mutant cannot induce
indole, but complementation of the mutant strain with the wild-type gene restored its ability to induce
indole production.
Indole tolerance assays indicated that the amount of
indole required to inhibit growth of most gut-protective bacteria was within the range detected in the CDI stools. We think that a high
indole level limits the growth of beneficial
indole-sensitive bacteria in the colon and alters colonization resistance and this might allow C. difficile to proliferate and persist. Together, these results reveal a unique mechanism of C. difficile persistence and provide insight into complex interactions and chemical warfare among the gut microbiota. IMPORTANCE
Clostridium difficile infection is the leading cause of hospital-acquired and
antibiotic-associated
diarrhea worldwide. C. difficile flourishes in the colon after the diversity of the beneficial and protective gut microbiota have been altered by
antibiotic therapy. C. difficile tends to persist, as does
dysbiosis, encouraging recurrence a few days to weeks
after treatment, and this further complicates treatment options. Here, we show that C. difficile might persist by manipulating the indigenous microbiota to produce
indole, a bioactive molecule that inhibits the growth and reconstitution of the protective gut microbiota during
infection. This discovery may explain a unique strategy C. difficile uses to control other bacteria in the colon and provide insight into the complex interactions and chemical warfare among the gut microbiota.