2,153
Views
5
CrossRef citations to date
0
Altmetric
Research Paper

The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome

, MBBS ORCID Icon ORCID Icon, , MBBS, PhD & , PhD
Pages 477-485 | Received 27 Nov 2017, Accepted 01 Mar 2018, Published online: 05 Sep 2018

References

  • Halfvarson J, Brislawn CJ, Lamendella R, Vazquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, et al. Dynamics of the human gut microbiome in inflammatory bowel disease. Nat Microbiol. 2017;2:17004. doi:10.1038/nmicrobiol.2017.4. PMID:28191884.
  • Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity. 2014;40:843–54. doi:10.1016/j.immuni.2014.05.013. PMID:24950204.
  • Dalal SR, Chang EB. The microbial basis of inflammatory bowel diseases. J Clin Invest. 2014;124:4190–6. doi:10.1172/JCI72330. PMID:25083986.
  • Butto LF, Haller D. Dysbiosis in crohn's disease – joint action of stochastic injuries and focal inflammation in the gut. Gut Microbes. 2017;8:53–8. doi:10.1080/19490976.2016.1270810. PMID:28102757.
  • Nagao-Kitamoto H, Kamada N. Host-microbial cross-talk in inflammatory bowel disease. Immune Netw. 2017;17:1–12. doi:10.4110/in.2017.17.1.1. PMID:28261015.
  • Lin L, Zhang J. Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol. 2017;18:2. doi:10.1186/s12865-016-0187-3. PMID:28061847.
  • Sartor RB, Wu GD. Roles for intestinal bacteria, viruses, and fungi in pathogenesis of inflammatory bowel diseases and therapeutic approaches. Gastroenterology. 2017;152:327–39 e4. doi:10.1053/j.gastro.2016.10.012. PMID:27769810.
  • Cohen NA, Maharshak N. Novel indications for fecal microbial transplantation: Update and review of the literature. Dig Dis Sci. 2017;62:1131–1145. doi:10.1007/s10620-017-4535-9.
  • Wright EK, Kamm MA, Teo SM, Inouye M, Wagner J, Kirkwood CD. Recent advances in characterizing the gastrointestinal microbiome in crohn's disease: A systematic review. Inflamm Bowel Dis. 2015;21:1219–28. PMID:25844959.
  • Machiels K, Joossens M, Sabino J, De Preter V, Arijs I, Eeckhaut V, Ballet V, Claes K, Van Immerseel F, Verbeke K, et al. A decrease of the butyrate-producing species roseburia hominis and faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut. 2014;63:1275–83. doi:10.1136/gutjnl-2013-304833. PMID:24021287.
  • Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Dore J. Low counts of faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis. 2009;15:1183–9. doi:10.1002/ibd.20903. PMID:19235886.
  • Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489:220–30. doi:10.1038/nature11550. PMID:22972295.
  • Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, et al. Moving pictures of the human microbiome. Genome Biol. 2011;12:R50. doi:10.1186/gb-2011-12-5-r50. PMID:21624126.
  • Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16s rrna sequencing. PLoS Biol. 2008;6:e280. doi:10.1371/journal.pbio.0060280. PMID:19018661.
  • Higuchi LM, Khalili H, Chan AT, Richter JM, Bousvaros A, Fuchs CS. A prospective study of cigarette smoking and the risk of inflammatory bowel disease in women. Am J Gastroenterol. 2012;107:1399–406. doi:10.1038/ajg.2012.196. PMID:22777340.
  • Nelson AM, Walk ST, Taube S, Taniuchi M, Houpt ER, Wobus CE, Young VB. Disruption of the human gut microbiota following norovirus infection. PLoS One. 2012;7:e48224. doi:10.1371/journal.pone.0048224. PMID:23118957.
  • Consortium HMP. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14. doi:10.1038/nature11234. PMID:22699609.
  • Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, et al. The treatment-naive microbiome in new-onset crohn's disease. Cell Host Microbe. 2014;15:382–92. doi:10.1016/j.chom.2014.02.005. PMID:24629344.
  • Lin JF, Chen JM, Zuo JH, Yu A, Xiao ZJ, Deng FH, Nie B, Jiang B. Meta-analysis: Fecal calprotectin for assessment of inflammatory bowel disease activity. Inflamm Bowel Dis. 2014;20:1407–15. doi:10.1097/MIB.0000000000000057. PMID:24983982.
  • van Rheenen PF, Van de Vijver E, Fidler V. Faecal calprotectin for screening of patients with suspected inflammatory bowel disease: Diagnostic meta-analysis. BMJ. 2010;341:c3369. doi:10.1136/bmj.c3369. PMID:20634346.
  • Kopylov U, Yung DE, Engel T, Avni T, Battat R, Ben-Horin S, Plevris JN, Eliakim R, Koulaouzidis A. Fecal calprotectin for the prediction of small-bowel crohn's disease by capsule endoscopy: A systematic review and meta-analysis. Eur J Gastroenterol Hepatol. 2016;28:1137–44. doi:10.1097/MEG.0000000000000692. PMID:27415156.
  • Panes J, Jairath V, Levesque BG. Advances in use of endoscopy, radiology, and biomarkers to monitor inflammatory bowel diseases. Gastroenterology. 2017;152:362–73 e3. doi:10.1053/j.gastro.2016.10.005. PMID:27751880.
  • Wright EK, Kamm MA, Wagner J, Teo SM, De Cruz P, Hamilton AL, Ritchie KJ, Inouye M, Kirkwood CD. Microbial factors associated with post-operative crohn's disease recurrence. J Crohns Colitis. 2017;11:191–203. PMID:27466174.
  • Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, Prince J, Kumar A, Sauer C, Zwick ME, et al. Dysbiosis, inflammation, and response to treatment: A longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med. 2016;8:75. doi:10.1186/s13073-016-0331-y. PMID:27412252.
  • Wills ES, Jonkers DM, Savelkoul PH, Masclee AA, Pierik MJ, Penders J. Fecal microbial composition of ulcerative colitis and crohn's disease patients in remission and subsequent exacerbation. PLoS One. 2014;9:e90981. doi:10.1371/journal.pone.0090981. PMID:24608638.
  • Martinez C, Antolin M, Santos J, Torrejon A, Casellas F, Borruel N, Guarner F, Malagelada JR. Unstable composition of the fecal microbiota in ulcerative colitis during clinical remission. Am J Gastroenterol. 2008;103:643–8. doi:10.1111/j.1572-0241.2007.01592.x. PMID:18341488.
  • Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, Finlay BB. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of enterobacteriaceae. Cell Host Microbe. 2007;2:204. doi:10.1016/j.chom.2007.08.002. PMID:18030708.
  • Clarke SF, Murphy EF, O'Sullivan O, Lucey AJ, Humphreys M, Hogan A, Hayes P, O'Reilly M, Jeffery IB, Wood-Martin R, et al. Exercise and associated dietary extremes impact on gut microbial diversity. Gut. 2014;63:1913–20. doi:10.1136/gutjnl-2013-306541. PMID:25021423.
  • Murtaza N, P OC, Morrison M. Diet and the microbiome. Gastroenterol Clin North Am. 2017;46:49–60. doi:10.1016/j.gtc.2016.09.005. PMID:28164852.
  • O'Brien CL, Allison GE, Grimpen F, Pavli P. Impact of colonoscopy bowel preparation on intestinal microbiota. PLoS One. 2013;8:e62815. doi:10.1371/journal.pone.0062815. PMID:23650530.
  • Pigneur B, Sokol H. Fecal microbiota transplantation in inflammatory bowel disease: The quest for the holy grail. Mucosal Immunol. 2016;9:1360–5. doi:10.1038/mi.2016.67. PMID:27461176.
  • Li YT, Cai HF, Wang ZH, Xu J, Fang JY. Systematic review with meta-analysis: Long-term outcomes of faecal microbiota transplantation for clostridium difficile infection. Aliment Pharmacol Ther. 2016;43:445–57. doi:10.1111/apt.13492. PMID:26662643.
  • Baillie JK, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y, et al. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genet. 2017;13:e1006641. doi:10.1371/journal.pgen.1006641. PMID:28263993.
  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41. doi:10.1128/AEM.01541-09. PMID:19801464.
  • Schloss PD, Gevers D, Westcott SL. Reducing the effects of pcr amplification and sequencing artifacts on 16s rrna-based studies. PLoS One. 2011;6:e27310. doi:10.1371/journal.pone.0027310. PMID:22194782.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. Uchime improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–200. doi:10.1093/bioinformatics/btr381. PMID:21700674.
  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. The silva ribosomal rna gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6. doi:10.1093/nar/gks1219. PMID:23193283.
  • Yue JC, Clayton MK. A similarity measure based on species proportions. Communications in Statistics – Theory and Methods. 2005;34:2123–31. doi:10.1080/STA-200066418..
  • R Core Team: R: A language and environment for statistical computing, 2016. [Accessed 26 October 2017]. https://www.r-project.org/.
  • White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol. 2009;5:e1000352. doi:10.1371/journal.pcbi.1000352. PMID:19360128.
  • Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, et al. Predictive functional profiling of microbial communities using 16s rrna marker gene sequences. Nat Biotechnol. 2013;31:814–21. doi:10.1038/nbt.2676. PMID:23975157.
  • Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60. doi:10.1186/gb-2011-12-6-r60. PMID:21702898.