An altered composition of the microbiome in microscopic colitis is driven towards the composition in healthy controls by treatment with budesonide

References

• Chande N, Al Yatama N, Bhanji T, et al. Interventions for treating lymphocytic colitis. Cochrane Database Syst Rev. 2017;7:CD006096.
   PubMed Web of Science ®Google Scholar
• Kafil T, Nguyen T, Patton P, et al. Interventions for treating collagenous colitis. Cochrane Database Syst Rev. 2017;11:CD003575.
   PubMed Web of Science ®Google Scholar
• Bonderup OK, Wigh T, Nielsen GL, et al. The epidemiology of microscopic colitis: a 10-year pathology-based nationwide Danish cohort study. Scand J Gastroenterol. 2015;50:393–398.
   PubMed Web of Science ®Google Scholar
• Jarnerot G, Tysk C, Bohr J, et al. Collagenous colitis and fecal stream diversion. Gastroenterology. 1995;109:449–455.
   PubMed Web of Science ®Google Scholar
• Münch A, Söderholm JD, Wallon C, et al. Dynamics of mucosal permeability and inflammation in collagenous colitis before, during, and after loop ileostomy. Gut. 2005;54:1126–1128.
   PubMed Web of Science ®Google Scholar
• Daferera N, Kumawat AK, Hultgren-Hörnquist E, et al. Fecal stream diversion and mucosal cytokine levels in collagenous colitis: a case report. World J Gastroenterol. 2015;21:6065–6071.
   PubMed Web of Science ®Google Scholar
• Kamada N, Núñez G. Regulation of the immune system by the resident intestinal bacteria. Gastroenterology. 2014;146:1477–1488.
   PubMed Web of Science ®Google Scholar
• Fischer H, Holst E, Karlsson F, et al. Altered microbiota in microscopic colitis. Gut. 2015;64:1185–1186.
   PubMed Web of Science ®Google Scholar
• Helal TE, Ahmed NS, El Fotoh OA. Lymphocytic colitis: a clue to bacterial etiology. World J Gastroenterol. 2005;11:7266–7271.
   PubMed Web of Science ®Google Scholar
• Magro F, Langner C, Driessen A, et al. European consensus on the histopathology of inflammatory bowel disease. J Crohns Colitis. 2013;7:827–851.
   PubMed Web of Science ®Google Scholar
• Hjortswang H, Tysk C, Bohr J, et al. Defining clinical criteria for clinical remission and disease activity in collagenous colitis. Inflamm Bowel Dis. 2009;15:1875–1881.
   PubMed Web of Science ®Google Scholar
• Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–998.
   PubMed Web of Science ®Google Scholar
• Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–7541.
   PubMed Web of Science ®Google Scholar
• Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:590–596.
   PubMed Web of Science ®Google Scholar
• Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005;71:8228–8235.
   PubMed Web of Science ®Google Scholar
• Lozupone C, Lladser ME, Knights D, et al. UniFrac: an effective distance metric for microbial community comparison. Isme J. 2011;5:169–172.
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc. 1995;57:289–300.
   Google Scholar
• Bäckhed F, Fraser CM, Ringel Y, et al. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe. 2012;12:611–622.
   PubMed Web of Science ®Google Scholar
• Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel diseases: current status and the future ahead. Gastroenterology 2014;146:1489–1499.
   PubMed Web of Science ®Google Scholar
• de Vos WM. Microbe profile: Akkermansia muciniphila: a conserved intestinal symbiont that acts as the gatekeeper of our mucosa. Microbiol. 2017;163:646–648.
   PubMed Web of Science ®Google Scholar
• Camarero C, Leon F, Colino E, et al. Collagenous colitis in children: clinicopathologic, microbiologic, and immunologic features. J Pediatr Gastroenterol Nutr. 2003;37:508–513.
   PubMed Web of Science ®Google Scholar
• Goff JS, Barnett JL, Pelke T, et al. Collagenous colitis: histopathology and clinical course. Am J Gastroenterol. 1997;92:57–60.
   PubMed Web of Science ®Google Scholar
• Yuan S, Reyes V, Bronner MP. Pseudomembranous collagenous colitis. Am J Surg Pathol. 2003;27:1375–1379.
   PubMed Web of Science ®Google Scholar
• Khan MA, Brunt EM, Longo WE, et al. Persistent Clostridium difficile colitis: a possible etiology for the development of collagenous colitis. Dig Dis Sci. 2000;45:998–1001.
   PubMed Web of Science ®Google Scholar
• Erim T, Alazmi WM, O'Loughlin CJ, et al. Collagenous colitis associated with Clostridium difficile: a cause effect? Dig Dis Sci 2003;48:1374–1375.
   PubMed Web of Science ®Google Scholar
• Shaz BH, Reddy SI, Ayata G, et al. Sequential clinical and histopathological changes in collagenous and lymphocytic colitis over time. Mod Pathol. 2004;17:395–401.
   PubMed Web of Science ®Google Scholar
• Makinen M, Niemela S, Lehtola J, et al. Collagenous colitis and Yersinia enterocolitica infection. Dig Dis Sci. 1998;43:1341–1346.
   PubMed Web of Science ®Google Scholar
• Bohr J, Nordfelth R, Jarnerot G, et al. Yersinia species in collagenous colitis: a serologic study. Scand J Gastroenterol. 2002;37:711–714.
   PubMed Web of Science ®Google Scholar
• Tamboli CP, Good MR, Reynolds EM, et al. Anti-Yersinia antibodies are not associated with microscopic colitis in an American case-control study. Scand J Gastroenterol. 2011;46:1442–1448.
   PubMed Web of Science ®Google Scholar
• Vandeputte D, Falony G, Vieira-Silva S, et al. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. 2016;65:57–62.
   PubMed Web of Science ®Google Scholar
• Krogsgaard LR, Engsbro AL, Stensvold CR, et al. The prevalence of intestinal parasites is not greater among individuals with irritable bowel syndrome: a population-based case-control study. Clin Gastroenterol Hepatol. 2015;13:507–513.
   PubMed Web of Science ®Google Scholar
• Petersen AM, Stensvold CR, Mirsepasi H, et al. Active ulcerative colitis associated with low prevalence of Blastocystis and Dientamoeba fragilis infection. Scand J Gastroenterol. 2013;48:638–639.
   PubMed Web of Science ®Google Scholar
• Norman JM, Handley SA, Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology. 2014;146:1459–1469.
   PubMed Web of Science ®Google Scholar
• Audebert C, Even G, Cian A, et al. Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Sci Rep. 2016;6:25255.
   PubMed Web of Science ®Google Scholar
• Andersen LOB, Bonde I, Nielsen HB, et al. A retrospective metagenomics approach to studying Blastocystis. FEMS Microbiol Ecol. 2015;91:1–9.
   Web of Science ®Google Scholar
• Krogsgaard L, O’brien Andersen L, Bech Johannesen T, et al. Characteristics of the bacterial microbiome in association with common intestinal parasites in irritable bowel syndrome. Clin Transl Gastroenterol. 2018;9:161.
   PubMed Web of Science ®Google Scholar
• Madisch A, Miehlke S, Bartosch F, et al. Microscopic colitis: clinical presentation, treatment and outcome of 494 patients. Z Gastroenterol. 2014;52:1062–1065.
   PubMed Web of Science ®Google Scholar
• Huang EY, Inoue T, Leone VA, et al. Using corticosteroids to reshape the gut microbiome: Implications for. Inflamm Bowel Dis. 2015;21:963–972.
   PubMed Web of Science ®Google Scholar
• Wu T, Yang L, Jiang J, et al. Chronic glucocorticoid treatment induced circadian clock disorder leads to lipid metabolism and gut microbiota alterations in rats. Life Sci. 2018;192:173–182.
   PubMed Web of Science ®Google Scholar
• Burke KE, Ananthakrishnan AN, Lochhead P, et al. Smoking is associated with an increased risk of microscopic colitis: results from two large prospective cohort studies of US women. J Crohns Colitis. 2018;12:559–567.
   PubMed Web of Science ®Google Scholar
• Pardi DS, Kelly CP. Microscopic colitis. Gastroenterology. 2011;140:1155–1165.
   PubMed Web of Science ®Google Scholar
• Capurso G, Lahner E. The interaction between smoking, alcohol and the gut microbiome. Best Pract Res Clin Gastroenterol. 2017;31:579–588.
   PubMed Web of Science ®Google Scholar
• Le Bastard Q, Al-Ghalith GA, Grégoire M, et al. Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications. Aliment Pharmacol Ther. 2018;47:332–345.
   PubMed Web of Science ®Google Scholar
• Imhann F, Bonder MJ, Vila AV, et al. Proton pump inhibitors affect the gut microbiome. Gut. 2016;65:740–748.
   PubMed Web of Science ®Google Scholar