Molecular Characterization and Spatial Analysis of a Simplified Gut Microbiota Displaying Colonization Resistance against Clostridium difficile

Abstract

The gut microbiota naturally protects the host against infections by pathogens. This microbiota can be disrupted in case of antibiotic treatments leading to the loss of the barrier effect and consequently to new colonization and opportunistic infections. We previously developed in our laboratory a trixenic mouse model microbiota displaying colonization resistance against Clostridium difficile. In this study, we used whole cell fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes in order to better evaluate the composition of this barrier flora and the spatial localization of each species. Flow cytometry technique in combination with FISH permitted to accurately quantify each species confirming the major contribution of a new species we named Clostridium "fusiformis". Transmission electron microscopy (TEM) and FISH combined with image analysis on tissue sections permitted to show that the previously unidentified species conferring the barrier effect is flagellated and deeply implanted in the crypts.

• Simplified Gut Microbiota
• Mouse Model
• Clostridium Difficile
• Rrna Probes
• Fluorescence In Situ Hybridization
• Flow Cytometry