Piglet Gut Microbiota under IBD Challenge Raw sequence reads

Inflammatory bowel diseases (IBD) including Crohn’s disease and Ulcerative colitis (UC), are chronic conditions characterized by recurrent episodes of intestinal inflammation. Adherent invasive Escherichia coli (AIEC) pathotype, has been increasingly implicated in the etiopathogenesis of IBD. We investigated effects of AIEC strain UM146 colonization on ileal, cecal, ascending and descending colon microbial profile in a pig model of experimental colitis. Carrageenan gum was used to mimic colitis in weaner piglets whereas AIEC strain UM146 previously isolated from CD patients was included to investigate a cause or consequence effect in IBD. Treatments were: 1) control , 2) carrageenan gum; CG, 3) AIEC strain UM146, and 4) CG+UM146. Pigs in 2 and 4 recived 1% CG in drinking water from day one whilst pigs in 3 and 4 were infected with UM146 on day 8. All pigs were euthanized on day 21. Tissue mucosal scrapings were used for DNA extraction and the V4 region of bacterial 16S rRNA was subjected to Illumina sequencing. Diversity measures, differences at phylum and genus levels, short chain fatty acids and tissue inflammatory cytokines were determined. CG-induced colitis decreased bacterial species richness and shifted community composition. At phylum level, we observed differences in CG and CGUM146 compared to control and UM146 including an increase in Proteobacteria and Deferribacteres and a decrease in Firmicutes, Actibobacteria, and Bacteroidetes in some intestinal sections. Specific taxa were associated with various treatments at lower phylogenetic levels, and microbial function was also altered in CG and CGUM146 compared to UM146 and control in the colon. We demonstrate that CG induced bacterial dysbiosis and shifted community composition at phylum and lower taxonomical levels, however, the effect of AIEC strain UM146 alone was not clear and did not vary much from the control.