Transcriptional responses of colon tissues following ex-vivo colonization with human microbiome

Purpose: The goal of this study is to compare colonic transcriptional responses following ex-vivo colonization with fecal samples collected from multiple sclerosis patients, before and after Propionic acid treatment and between the patients that responded or not to the therapy. Methods: Bulk whole-tissue mRNA profiles of 13-day-old wild-type mice colons were generated by deep sequencing, in triplicate, using Illumina NextSeq platform. Overall design: To test whether changes to microbiome composition as a result of PA intake have functional consequences on the local gut tissue, fecal samples of patients before and after 14 days of PA intake were assessed in an intestinal organ culture system (Yissachar et al., 2017). For the analysis, MS patients microbiome of responders (n=5) and non-responders (n=4), before- and after-PA intake, was introduced into the gut culture system at equivalent bacterial load (10^7 CFU/ml) and bulk RNA sequencing of colon tissues was conducted after 2 hours ( total of 36 colon samples, in two independent sequencing runs).