eHealth: Disease activity measures are related to the faecal gut microbiota in adult patients with ulcerative colitis

References

• Lane ER, Zisman TL, Suskind DL. The microbiota in inflammatory bowel disease: current and therapeutic insights. J Inflamm Res. 2017;10:63–73.
   PubMed Web of Science ®Google Scholar
• Langholz E. Ulcerative colitis. An epidemiological study based on a regional inception cohort, with special reference to disease course and prognosis. Dan Med Bull. 1999;46(5):400–415.
   PubMed Web of Science ®Google Scholar
• Munkholm P. Crohn’s disease-occurrence course and prognosis. An epidemiologic cohort-study. Dan Med Bull. 1997;44(3):287–302.
   PubMed Web of Science ®Google Scholar
• Burisch J, Kiudelis G, Kupcinskas L, et al. Natural disease course of Crohn’s disease during the first 5 years after diagnosis in a European population-based inception cohort: an Epi-IBD study. Gut. 2019;68(3):423–433.
   PubMed Web of Science ®Google Scholar
• Elkjaer M, Shuhaibar M, Burisch J, et al. E-health empowers patients with ulcerative colitis: a randomised controlled trial of the web-guided 'Constant-care' approach. Gut. 2010;59(12):1652–1661.
   PubMed Web of Science ®Google Scholar
• Burisch J, Munkholm P. Telemonitoring and self-care in patients with IBD. In: Cross RK, Watson AR, editors. Telemanagement of inflammatory bowel disease. Cham (Switzerland): Springer International Publishing AG; 2015. p. 85–100.
   Google Scholar
• Vinding KK, Elsberg H, Thorkilgaard T, et al. Fecal calprotectin measured by patients at home using smartphones-a new clinical tool in monitoring patients with inflammatory bowel disease. Inflamm Bowel Dis. 2016;22(2):336–344.
   PubMed Web of Science ®Google Scholar
• Haisma S-M, Galaurchi A, Almahwzi S, et al. P625 Head-to-head comparison of three stool calprotectin tests for home use. J Crohn’s Colitis. 2019;13(Supplement_1):S430–S430.
   Google Scholar
• Ankersen DV, Weimers P, Burisch J. Whats 'App-ening': the help of new technologies in nutrition in digestive diseases. Curr Opin Clin Nutr Metab Care. 2017;20(5):426–431.
   PubMed Web of Science ®Google Scholar
• De Vos M, Louis EJ, Jahnsen J, et al. Consecutive fecal calprotectin measurements to predict relapse in patients with ulcerative colitis receiving infliximab maintenance therapy. Inflamm Bowel Dis. 2013;19(10):2111–2117.
   Web of Science ®Google Scholar
• Theede K, Holck S, Ibsen P, et al. Fecal calprotectin predicts relapse and histological mucosal healing in ulcerative colitis. Inflamm Bowel Dis. 2016;22(5):1042–1048.
   PubMed Web of Science ®Google Scholar
• Ankersen DV, Carlsen K, Marker D, et al. Using eHealth strategies in delivering dietary and other therapies in patients with irritable bowel syndrome and inflammatory bowel disease. J Gastroenterol Hepatol. 2017;32:27–31.
   PubMed Web of Science ®Google Scholar
• Hansen JJ, Sartor RB. Therapeutic manipulation of the microbiome in IBD: current results and future approaches. Curr Treat Options Gastroenterol. 2015;13(1):105–120.
   PubMedGoogle Scholar
• Bernstein CN, Forbes JD. Gut microbiome in inflammatory bowel disease and other chronic immune-mediated inflammatory diseases. Inflamm Intest Dis. 2017;2(2):116–123.
   PubMedGoogle Scholar
• Franzosa EA, Sirota-Madi A, Avila-Pacheco J, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019;4(2):293–305.
   PubMed Web of Science ®Google Scholar
• Ankersen DV, Weimers PM, et al. Individualized home-monitoring of disease activity in adult patients with inflammatory bowel disease can be recommended in clinical practice: a randomized-clinical trial. World J Gastroenterol. 2019;25(40):6158–6171.
   PubMed Web of Science ®Google Scholar
• Jowett SL, Jowett SL, Jowett SL, et al. Defining relapse of ulcerative colitis using a symptom-based activity index. Scand J Gastroenterol. 2003;38(2):164–171.
   PubMed Web of Science ®Google Scholar
• Best WR. Predicting the Crohn's disease activity index from the Harvey-Bradshaw Index. Inflamm Bowel Dis. 2006;12(4):304–310.
   PubMed Web of Science ®Google Scholar
• Silverberg MS, Satsangi J, Ahmad T, et al. Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: report of a working party of the 2005 Montreal World Congress of Gastroenterology. Can J Gastroenterol. 2005;19(Suppl A):5A–36A.
   PubMed Web of Science ®Google Scholar
• Satsangi J, Silverberg MS, Vermeire S, et al. The Montreal classification of inflammatory bowel disease: controversies, consensus, and implications. Gut. 2006;55(6):749–753.
   PubMed Web of Science ®Google Scholar
• Casén C, Vebø HC, Sekelja M, et al. Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD. Aliment Pharmacol Ther. 2015;42(1):71–83.
   PubMed Web of Science ®Google Scholar
• Klindworth A, Pruesse E, Schweer T, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1.
   PubMed Web of Science ®Google Scholar
• R Development Core Team R. R: A language and environment for statistical computing; 2008. http://softlibre.unizar.es/manuales/aplicaciones/r/fullrefman.pdf
   Google Scholar
• McMurdie PJ, Holmes S. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.
   PubMed Web of Science ®Google Scholar
• Oksanen AJ, Blanchet FG, Friendly M, et al. Package “vegan” (Version 2.5-6). 2019. https://cran.r-project.org/web/packages/vegan/vegan.pdf
   Google Scholar
• Warnes GR, Bolker B, Bonebakker L, et al. Package “gplots”: Various R programming tools for plotting data. 2020. https://cran.r-project.org/web/packages/gplots/gplots.pdf
   Google Scholar
• Wickham H. ggplot2. Springer US, New York 2009.
   Google Scholar
• Sievert C, Parmer C, Hocking T, et al. Package “plotly.” Version (4.9.2.1). 2020. https://CRAN.R-project.org/package=plotly
   Google Scholar
• Bates D, Mächler M, Bolker B, et al. Fitting linear mixed-effects models using lme4. J Statist Softw. 2015;67(1):1–48.
   Google Scholar
• Blum HE. The Microbiome: a key player in human health and disease. J Healthc Commun. 2017;2(3):1–5.
   Google Scholar
• Qin J, Li R, Raes J, MetaHIT Consortium, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
   PubMed Web of Science ®Google Scholar
• Halfvarson J, Brislawn CJ, Lamendella R, et al. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol. 2017;2(5):17004.
   PubMed Web of Science ®Google Scholar
• Ananthakrishnan AN, Luo C, Yajnik V, et al. Gut microbiome function predicts response to anti-integrin biologic therapy in inflammatory bowel diseases. Cell Host Microbe. 2017;21(5):603–610.e3.
   PubMed Web of Science ®Google Scholar
• Morgan XC, Tickle TL, Sokol H, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13(9):R79.
   PubMed Web of Science ®Google Scholar
• Lewis JD. The utility of biomarkers in the diagnosis and therapy of inflammatory bowel disease. Gastroenterology. 2011;140(6):1817–1826.e2.
   PubMed Web of Science ®Google Scholar
• Carlsen K, Riis LB, Elsberg H, et al. The sensitivity of fecal calprotectin in predicting deep remission in ulcerative colitis. Scand J Gastroenterol. 2018;53(7):825–830.
   PubMed Web of Science ®Google Scholar
• Alibrahim B, Aljasser MI, Salh B. Fecal calprotectin use in inflammatory bowel disease and beyond: a mini-review. Can J Gastroenterol Hepatol. 2015;29(3):157–163.
   PubMed Web of Science ®Google Scholar
• Murphy EC, Frick IM. Gram-positive anaerobic cocci – commensals and opportunistic pathogens. FEMS Microbiol Rev. 2013;37(4):520–553.
   PubMed Web of Science ®Google Scholar
• Brook I. Peptostreptococcal infection in children. Scand J Infect Dis. 1994;26(5):503–510.
   PubMed Web of Science ®Google Scholar
• Prosberg M, Bendtsen F, Vind I, et al. The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis. Scand J Gastroenterol. 2016;51(12):1407–1415.
   PubMed Web of Science ®Google Scholar
• Machiels K, Joossens M, Sabino J, et al. A decrease of the butyrate-producing species roseburia hominis and faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut. 2014;63(8):1275–1283.
   PubMed Web of Science ®Google Scholar
• Tsoi H, Chu ESH, Zhang X, et al. Peptostreptococcus anaerobius induces intracellular cholesterol biosynthesis in colon cells to induce proliferation and causes dysplasia in mice. Gastroenterology. 2017;152(6):1419–1433.e5.
   PubMed Web of Science ®Google Scholar
• Dejea CM, Fathi P, Craig JM, et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science. 2018;359(6375):592–597.
   PubMed Web of Science ®Google Scholar
• Lloyd-Price J, Arze C, Ananthakrishnan AN, IBDMDB Investigators, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655–662.
   PubMed Web of Science ®Google Scholar
• Chen SJ, Liu XW, Liu JP, et al. Ulcerative colitis as a polymicrobial infection characterized by sustained broken mucus barrier. World J Gastroenterol. 2014;20(28):9468–9475.
   PubMed Web of Science ®Google Scholar