Characterisation and therapeutic manipulation of the gut microbiome in inflammatory bowel disease

Internal Medicine Journal

Volumn 46, Issue 3, 2016, Pages 266-273

  Schulberg, J ^a   De Cruz, P ^a,b  

^a AUSTIN HOSPITAL   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Antibiotics; Crohn disease; Faecal microbiota transplantation; Microbiota; Prebiotics; Probiotics; Ulcerative colitis

Indexed keywords

ANTIBIOTIC AGENT; DNA; MEMBRANE PROTEIN; PREBIOTIC AGENT; RNA; ANTIINFECTIVE AGENT; PROBIOTIC AGENT;

ARTICLE; BIOMICS; DIETARY INTAKE; DYSBIOSIS; ENVIRONMENTAL FACTOR; FECES MICROFLORA; GENETICS; GEOGRAPHY; HOST; IMMUNE SYSTEM; IMMUNITY; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; LIFESTYLE; METABOLITE; METABOLOMICS; METAGENOMICS; METAPROTEONOMIC; METATRANSCRIPTOMIC; PRIORITY JOURNAL; SYMBIOSIS; TRANSCRIPTOMICS; TRANSPLANTATION; ANIMAL; DRUG EFFECTS; HUMAN; INFLAMMATORY BOWEL DISEASES; MICROBIOLOGY; PHYSIOLOGY;

ANIMALS; ANTI-BACTERIAL AGENTS; GASTROINTESTINAL MICROBIOME; HUMANS; INFLAMMATORY BOWEL DISEASES; PROBIOTICS;

EID: 84960120201     PISSN: 14440903     EISSN: 14455994     Source Type: Journal    
DOI: 10.1111/imj.13003     Document Type: Article

References (58)

1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007; 449: 804-10.
2. Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 2014; 32: 834-41.
3. Sokol H, Seksik P. The intestinal microbiota in inflammatory bowel diseases: time to connect with the host. Curr Opin Gastroenterol 2010; 26: 327-31.
4. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008; 6: 776-88.
5. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
6. Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N et al. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 2011; 11: 7.
7. Abubakar I, Myhill D, Aliyu SH, Hunter PR. Detection of Mycobacterium avium subspecies paratuberculosis from patients with Crohn's disease using nucleic acid-based techniques: a systematic review and meta-analysis. Inflamm Bowel Dis 2008; 14: 401-10.
8. Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, Barnich N et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 2004; 127: 412-21.
9. Norman JM, Handley SA, Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology 2014; 146: 1459-69.
10. Ott SJ, Kuhbacher T, Musfeldt M, Rosenstiel P, Hellmig S, Rehman A et al. Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand J Gastroenterol 2008; 43: 831-41.
11. De Cruz P, Prideaux L, Wagner J, Ng SC, McSweeney C, Kirkwood C et al. Characterization of the gastrointestinal microbiota in health and inflammatory bowel disease. Inflamm Bowel Dis 2012; 18: 372-90.
12. Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA 2008; 105: 2117-22.
13. Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS. Application of metagenomics in the human gut microbiome. World J Gastroenterol 2015; 21: 803-14.
14. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
15. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012; 13: R79.
16. Rehman A, Lepage P, Nolte A, Hellmig S, Schreiber S, Ott SJ. Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J Med Microbiol 2010; 59: 1114-22.
17. Redon E, Loubiere P, Cocaign-Bousquet M. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 2005; 280: 36380-5.
18. Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One 2012; 7: e49138.
19. Bictash M, Ebbels TM, Chan Q, Loo RL, Yap IK, Brown IJ et al. Opening up the "Black Box": metabolic phenotyping and metabolome-wide association studies in epidemiology. J Clin Epidemiol 2010; 63: 970-9.
20. Wellcome Trust Case Control Consortium. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 2007; 447: 661-78.
21. McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR et al. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome 2013; 1: 17.
22. Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 1999; 69: 1035S-45.
23. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA 2011; 108: 4578-85.
24. Savino F, Roana J, Mandras N, Tarasco V, Locatelli E, Tullio V. Faecal microbiota in breast-fed infants after antibiotic therapy. Acta Paediatr 2011; 100: 75-8.
25. Munyaka PM, Khafipour E, Ghia JE. External influence of early childhood establishment of gut microbiota and subsequent health implications. Front Pediatr 2014; 2: 109.
26. Zoetendal EG, Akkermans AD, De Vos WM. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 1998; 64: 3854-9.
27. Zhang J, Guo Z, Xue Z, Sun Z, Zhang M, Wang L et al. A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities. ISME J 2015; 9: 1979-90.
28. Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307: 1915-20.
29. Stewart JA, Chadwick VS, Murray A. Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children. J Med Microbiol 2005; 54: 1239-42.
30. Van Limbergen J, Radford-Smith G, Satsangi J. Advances in IBD genetics. Nat Rev Gastroenterol Hepatol 2014; 11: 372-85.
31. Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis 2011; 17: 179-84.
32. Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med 2014; 6: 107.
33. Bouskra D, Brezillon C, Berard M, Werts C, Varona R, Boneca IG et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 2008; 456: 507-10.
34. Hooper LV, Macpherson AJ. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat Rev Immunol 2010; 10: 159-69.
35. Duerkop BA, Vaishnava S, Hooper LV. Immune responses to the microbiota at the intestinal mucosal surface. Immunity 2009; 31: 368-76.
36. Cerf-Bensussan N, Gaboriau-Routhiau V. The immune system and the gut microbiota: friends or foes? Nat Rev Immunol 2010; 10: 735-44.
37. Schachtschneider KM, Yeoman CJ, Isaacson RE, White BA, Schook LB, Pieters M. Modulation of systemic immune responses through commensal gastrointestinal microbiota. PLoS One 2013; 8: e53969.
38. Prideaux L, Kang S, Wagner J, Buckley M, Mahar JE, De Cruz P et al. Impact of ethnicity, geography, and disease on the microbiota in health and inflammatory bowel disease. Inflamm Bowel Dis 2013; 19: 2906-18.
39. Fallani M, Young D, Scott J, Norin E, Amarri S, Adam R et al. Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. J Pediatr Gastroenterol Nutr 2010; 51: 77-84.
40. Xu Z, Knight R. Dietary effects on human gut microbiome diversity. Br J Nutr 2015; 113: S1-5.
41. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334: 105-8.
42. Lee D, Albenberg L, Compher C, Baldassano R, Piccoli D, Lewis JD et al. Diet in the pathogenesis and treatment of inflammatory bowel diseases. Gastroenterology 2015; 148: 1087-106.
43. Sartor RB. Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics. Gastroenterology 2004; 126: 1620-33.
44. Mimura T, Rizzello F, Helwig U, Poggioli G, Schreiber S, Talbot IC et al. Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis. Gut 2004; 53: 108-14.
45. Sood A, Midha V, Makharia GK, Ahuja V, Singal D, Goswami P et al. The probiotic preparation, VSL#3 induces remission in patients with mild-to-moderately active ulcerative colitis. Clin Gastroenterol Hepatol 2009; 7: 1202-9, 1209.e1.
46. Goldenberg JZ, Ma SS, Saxton JD, Martzen MR, Vandvik PO, Thorlund K et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev 2013; 5: CD006095.
47. Hutkins RW, Krumbeck JA, Bindels LB, Cani PD, Fahey G Jr, Goh YJ et al. Prebiotics: why definitions matter. Curr Opin Biotechnol 2015; 37: 1-7.
48. Gibson GR, Beatty ER, Wang X, Cummings JH. Selective stimulation of bifidobacteria in the human colon by oligofructose and inulin. Gastroenterology 1995; 108: 975-82.
49. Millard AL, Mertes PM, Ittelet D, Villard F, Jeannesson P, Bernard J. Butyrate affects differentiation, maturation and function of human monocyte-derived dendritic cells and macrophages. Clin Exp Immunol 2002; 130: 245-55.
50. Joossens M, De Preter V, Ballet V, Verbeke K, Rutgeerts P, Vermeire S. Effect of oligofructose-enriched inulin (OF-IN) on bacterial composition and disease activity of patients with Crohn's disease: results from a double-blinded randomised controlled trial. Gut 2012; 61: 958.
51. Benjamin JL, Hedin CR, Koutsoumpas A, Ng SC, McCarthy NE, Hart AL et al. Randomised, double-blind, placebo-controlled trial of fructo-oligosaccharides in active Crohn's disease. Gut 2011; 60: 923-9.
52. Perez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K et al. Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 2013; 62: 1591-601.
53. Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I et al. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell 2014; 158: 705-21.
54. Ungaro R, Bernstein CN, Gearry R, Hviid A, Kolho KL, Kronman MP et al. Antibiotics associated with increased risk of new-onset Crohn's disease but not ulcerative colitis: a meta-analysis. Am J Gastroenterol 2014; 109: 1728-38.
55. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013; 368: 407-15.
56. Kelly CR, Kahn S, Kashyap P, Laine L, Rubin D, Atreja A et al. Update on fecal microbiota transplantation 2015: indications, methodologies, mechanisms, and outlook. Gastroenterology 2015; 149: 223-37.
57. Moayyedi P, Surette MG, Kim PT, Libertucci J, Wolfe M, Onischi C et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology 2015; 149: 102-9.e6.
58. Rossen NG, Fuentes S, van der Spek MJ, Tijssen J, Hartman JH, Duflou A et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology 2015; 149: 110-8.e4.