Transcriptomic analysis of intestinal organoids, derived from pigs divergent in feed efficiency, and their response to Escherichia coli. Transcriptomic analysis of intestinal organoids

There is increasing interest in using intestinal organoids to study complex traits like feed efficiency (FE) and host-microbe interactions. The aim of this study was to investigate differences in molecular phenotype organoids derived from pigs divergent for FE as well as their responses to challenge with Escherichia coli (E. coli). Colon and ileum samples were collected from low and high FE pigs and two dimensional (2D) monolayer organoids were cultured. Organoid groups from low or high FE pigs were either challenged with E. coli or used as controls. Genome-wide gene expression was used to investigate molecular differences between pigs that were phenotypically divergent for FE and to study the difference in gene expression upon an E. coli challenged. We show 1) there are minor differences in colon organoid gene expressions between low and high FE phenotypes, 2) that an E. coli challenge results in a strong immune response in both colon and ileum organoids, 3) that this immune response seems to be less pronounced in the colon organoids of high FE pigs and 4) a slightly stronger immune response was observed in ileum than in colon organoids. These findings demonstrate the potential for using organoids to gain insights into complex biological mechanisms such as FE.