Antibiotic pre-treatment of an ulcerative colitis associated fecal microbial community does not improve integration of therapeutic bacteria in vitro (Illumina 16S sequencing data)

Fecal microbiota transplantation (FMT) is a proposedly useful strategy for the treatment of ulcerative colitis (UC) through remediation of the patient gut microflora. However, its therapeutic success has varied, necessitating research to uncover mechanisms that improve patient response. Antibiotic pre-treatment has been proposed as one method to enhance the success rate in UC by increasing niche availability for introduced species that can alter the underlying ecosystem. The purpose of this study was to use an in vitro, bioreactor-based, colonic ecosystem model to determine how pre-treatment with rifamixin, an antibiotic shown to be efficacious for the treatment of UC flares, influenced engraftment of bacterial strains sourced from a healthy donor into a defined microbial community representative of a UC patient fecal ecosystem.