The Effect of Gut Microbiota Variation on Clostridioides difficile Infection

Abstract

The bacteria, viruses, fungi, archaea, and protozoa, collectively known as microbiota, present throughout our intestine prevent the pathogenic bacteria Clostridioides difficile from infecting. This protection known as colonization resistance is lost when the gut microbiota is perturbed by antibiotics. This disruption opens a niche for C. difficile to colonize. C. difficile is removed with antibiotic treatment but that also leaves niches open for C. difficile to reinfect. There have been efforts to develop bacterial consortia to eliminate C. difficile and resolve the open niches. However, a few recent studies have revealed differences in C. difficile colonization associated with different perturbations. I hypothesized that, due to the variation in the gut microbiota and susceptibility to C. difficile infection (CDI), the gut microbiota has perturbation-specific effects on CDI. To test this hypothesis, I challenged mice with diverse gut microbiota, via either human fecal inoculation of germ-free mice or antibiotic treatments of conventional mice, to test whether microbiota variation affected disease severity, clearance of C. difficile colonization, or restoration of colonization resistance. In Chapter II, I varied the gut microbiota by colonizing germ-free mice with human fecal communities prior to C. difficile challenge. We then observed the effect of the gut microbiota variation on the resultant disease. These data showed that variation in the bacterial community associated with variation in moribundity and cecal tissue histopathology. In Chapter III, I varied the gut microbiota by treating to conventional mice from the same colony, containing a homogenous gut communities, with either clindamycin, cefoperazone, or streptomycin. I varied the antibiotic dose to permit C. difficile colonization and subsequent natural clearance to test whether the communities had similar changes in the gut bacterial community associated elimination of C. difficile. This set of experiments showed that the bacterial community undergoes antibiotic-specific changes concurrent with the elimination of C. difficile. In Chapter IV, I created variation in the gut microbiota with the three antibiotics previously used then tested whether a fecal community transplant (FCT) can restore colonization resistance. Mice treated with clindamycin became colonized and then cleared C. difficile, regardless if they received PBS or a FCT. Cefoperazone-treated mice were able to clear C. difficile colonization only when they received a FCT. Streptomycin-treated mice were able to resist colonization with a diluted FCT. These experiments showed the effectiveness of a simplified community, such as a diluted FCT, was specific to the antibiotic perturbation. My results show that the niche C. difficile occupies affects disease manifestation, the community changes associated with eliminating C. difficile colonization, and the bacteria necessary to fill the available niches to prevent colonization. These studies show that to prevent CDI we need to better understand the range in available niches in susceptible communities that C. difficile can occupy and the requirements to fill the available niches.