Spatial, genetic, and epigenetic regulation of intestinal Klebsiella and Enterococcus pathobionts

This study characterises Klebsiella and Enterococcus strains isolated from the appendix and multiple colonic regions of pediatric IBD patients. Strains from eight patients were collected, with detailed functional and genomic analyses performed on eight strains from two UC patients. Whole-genome sequencing, Oxford Nanopore Technologies, and intestinal epithelial assays reveal strain- and site-specific virulence, biofilm formation, invasion, and immune activation, which correlate with DNA methylation and genetic modifications. These findings show how environmental pressures in the gut influence microbial behaviour and are relevant to understanding host-microbe interactions in human disease. This repository contains analysis files for DNA methylation derived from Oxford Nanopore Technologies.