A Pig model of colitis intestinal tissues Raw sequence reads. pig gut metagenome

Introduction: Dysbiosis of intestinal gut microbiota has been associated with the pathogenesis of inflammatory bowel disease (IBD) which includes Chron’s disease and Ulcerative colitis. Current medical treatment of IBD involve the use of antibiotics and other compounds with anti-inflammatory properties; however, not all patients respond well to these therapies calling for alternative therapeutic measures. We investigated therapeutic role of potato resistant starch (prebiotic) and E. coli derived probiotics on the ileal, cecal, ascending and descending colon microbiota in a pig model of IBD. Methods: Carageenan gum (CG) was used to induce mild ulcers/colitis in the gastrointestinal tract. Thirty piglets received basal diet and were divided into 5 treatments: 1) control 2) CG only 3) CG+Prebiotic 4) CG+Probiotics E. coli strains UM2 and 7, and 5) CG+Prebiotic+Probiotics. Pigs in treatments 2 - 5 recived 1% CG in drinking water from d1 of experiment. Treatments 3 - 5 were offered from d8 of the study and all pigs were euthanized on d21. Tissue mucosal scrapings were used for DNA extraction and the V4 region of bacterial 16SrRNA was amplified and subjected to Illumina sequencing. Results: Microbial α-diversity was consistently lower in CG compared to the control but inclusion of the prebiotics, probiotics slightly improved species richness. Also, β-diversity differed among treatment groups especially in the cecum and descending colon. Firmicutes and Bacteroidetes decreased in most treatments compared to the control while Proteobacteria and Deferribacteres increased particularly in the ileum, cecum and descending colon. PLS-DA analysis revealed treatment differences at lower taxonomical levels when CG was compared with the therapeutic treatments suggesting that CG caused dysbiosis and that, resistant starch and E. coli derived probiotics might attenuate CG-induced bacterial changes in the GIT. Conclusion: The results indicate that CG may be effective in modeling colitis and that, resistant starch and to some extent the combination of resistant starch and the probiotics could attenuate bacterial dysbiosis and help in the development of beneficial bacteria in a pig model of experimental colitis.