Dysbiosis in the pathogenesis of pediatric inflammatory bowel diseases

International Journal of Inflammation

Volumn 2012, Issue , 2012, Pages

  Comito, Donatella ^a   Romano, Claudio ^a  

^a UNIVERSITY OF MESSINA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE IMMUNITY; BACTERICIDAL ACTIVITY; CHILDHOOD DISEASE; CROHN DISEASE; DYSBIOSIS; ENTERITIS; GENETIC PREDISPOSITION; HUMAN; IMMUNOPATHOGENESIS; INNATE IMMUNITY; INTESTINE FLORA; MICROBIAL POPULATION DYNAMICS; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; NONHUMAN; PRIORITY JOURNAL; REVIEW; SPECIES COMPOSITION; SYMBIOSIS; ULCERATIVE COLITIS;

EID: 84868137991     PISSN: 20908040     EISSN: 20420099     Source Type: Journal    
DOI: 10.1155/2012/687143     Document Type: Review

References (61)

1. Sauer C. G., Kugathasan S., Pediatric inflammatory bowel disease: highlighting pediatric differences in IBD. Gastroenterology Clinics of North America 2009 38 4 611 628 2-s2.0-70350749721 10.1016/j.gtc.2009.07.010
2. Kugathasan S., Judd R. H., Hoffmann R. G., Heikenen J., Telega G., Khan F., Weisdorf-Schindele S., San Pablo W., Perrault J., Park R., Yaffe M., Brown C., Rivera-Bennett M. T., Halabi I., Martinez A., Blank E., Werlin S. L., Rudolph C. D., Binion D. G., Epidemiologic and clinical characteristics of children with newly diagnosed inflammatory bowel disease in Wisconsin: a statewide population-based study. Journal of Pediatrics 2003 143 4 525 531 2-s2.0-0242330303 10.1067/S0022-3476(03)00444-X (Pubitemid 37352514)
3. Sun L., Nava G. M., Stappenbeck T. S., Host genetic susceptibility, dysbiosis, and viral triggers in inflammatory bowel disease. Current Opinion in Gastroenterology 2011 27 4 321 327 2-s2.0-79958816030 10.1097/MOG. 0b013e32834661b4
4. Walker A. W., Sanderson J. D., Churcher C., Parkes G. C., Hudspith B. N., Rayment N., Brostoff J., Parkhill J., Dougan G., Petrovska L., 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 Microbiology 2011 11, article 7 2-s2.0-78650973052 10.1186/1471-2180-11-7
5. Xavier R. J., Podolsky D. K., Unravelling the pathogenesis of inflammatory bowel disease. Nature 2007 448 7152 427 434 2-s2.0-34547176642 10.1038/nature06005 (Pubitemid 47123518)
6. Kaser A., Zeissig S., Blumberg R. S., Inflammatorybowel disease. Annual Review of Immunology 2009 28 573 621 10.1146/annurev-immunol-030409-101225
7. Domínguez-Bello M. G., Costello E. K., Contreras M., Magris M., Hidalgo G., Fierer N., Knight R., Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences of the United States of America 2010 107 26 11971 11975 2-s2.0-77955386857 10.1073/pnas.1002601107
8. Ley R. E., Peterson D. A., Gordon J. I., Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006 124 4 837 848 2-s2.0-32944466887 10.1016/j.cell.2006.02.017 (Pubitemid 43261456)
9. Domínguez-Bello M. G., Blaser M. J., Ley R. E., Knight R., Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 2011 140 6 1713 1719 2-s2.0-79955569490 10.1053/j.gastro.2011.02.011
10. Smith K., McCoy K. D., Macpherson A. J., Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Seminars in Immunology 2007 19 2 59 69 2-s2.0-34249284197 10.1016/j.smim.2006. 10.002 (Pubitemid 46810285)
11. Bach J. F., The effect of infections on susceptibility to autoimmune and allergic diseases. New England Journal of Medicine 2002 347 12 911 920 2-s2.0-0037136537 10.1056/NEJMra020100
12. Round J. L., Mazmanian S. K., The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology 2009 9 5 313 323 2-s2.0-67349250428 10.1038/nri2515
13. Mahowalda M. A., Reya F. E., Seedorfa H., Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proceedings of the National Academy of Sciences of the United States of America 2009 106 14 5859 5864
14. Knights D., Costello E. K., Knight R., Supervised classification of human microbiota. FEMS Microbiology Reviews 2011 35 2 343 359 2-s2.0-79251625980 10.1111/j.1574-6976.2010.00251.x
15. Chung H., Kasper D. L., Microbiota-stimulated immune mechanisms to maintain gut homeostasis. Current Opinion in Immunology 2010 22 4 455 460 2-s2.0-77955655862 10.1016/j.coi.2010.06.008
16. Abraham C., Medzhitov R., Interactions between the host innate immune system and microbes in inflammatory bowel disease. Gastroenterology 2011 140 6 1729 1737 2-s2.0-79955552936 10.1053/j.gastro.2011.02.012
17. Peterson D. A., McNulty N. P., Guruge J. L., Gordon J. I., IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host and Microbe 2007 2 5 328 339 2-s2.0-35848931007 10.1016/j.chom.2007.09.013 (Pubitemid 350056397)
18. Kaplan J. L., Shi H. N., Walker W. A., The role of microbes in developmental immunologic programming. Pediatric Research 2011 69 6 465 472 2-s2.0-79955789416 10.1203/PDR.0b013e318217638a
19. Feng T., Elson C. O., Cong Y., Treg cell-IgA axis in maintenance of host immune homeostasis with microbiota. International Immunopharmacology 2011 11 5 589 592 2-s2.0-79954631163 10.1016/j.intimp.2010.11.016
20. Ekbom A., Adami H. O., Helmick C. G., Jonzon A., Zack M. M., Perinatal risk factors for inflammatory bowel disease: a case-control study. American Journal of Epidemiology 1990 132 6 1111 1119 2-s2.0-0025652011
21. Matricon J., Barnich N., Ardid D., Immunopathogenesis of inflammatory bowel disease. Self/Nonself 2010 1 4 299 309. Landes Bioscience 2-s2.0-79851479595 10.4161/self.1.4.13560
22. Hildebrand H., Malmborg P., Askling J., Ekbom A., Montgomery S. M., Early-life exposures associated with antibiotic use and risk of subsequent Crohn's disease. Scandinavian Journal of Gastroenterology 2008 43 8 961 966 2-s2.0-47949129213 10.1080/00365520801971736
23. Elson C. O., Cong Y., McCracken V. J., Dimmitt R. A., Lorenz R. G., Weaver C. T., Experimental models of inflammatory bowel disease reveal innate, adaptive, and regulatory mechanisms of host dialogue with the microbiota. Immunological Reviews 2005 206 260 276 2-s2.0-23344449020 10.1111/j.0105-2896. 2005.00291.x (Pubitemid 41105175)
24. Scaldaferri F., Fiocchi C., Inflammatory bowel disease: progress and current concepts of etiopathogenesis. Journal of digestive diseases 2007 8 4 171 178 2-s2.0-38449113183 10.1111/j.1751-2980.2007.00310.x
25. Sokol H., Lay C., Seksik P., Tannock G. W., Analysis of bacterial bowel communities of IBD patients: what has it revealed? Inflammatory Bowel Diseases 2008 14 6 858 867 2-s2.0-46049086230 10.1002/ibd.20392 (Pubitemid 351898071)
26. Peterson D. A., Frank D. N., Pace N. R., Gordon J. I., Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host and Microbe 2008 3 6 417 427 2-s2.0-44649118583 10.1016/j.chom.2008.05.001 (Pubitemid 351773097)
27. Macfarlane S., Steed H., Macfarlane G. T., Intestinal bacteria and inflammatory bowel disease. Critical Reviews in Clinical Laboratory Sciences 2009 46 1 25 54 2-s2.0-58149132307 10.1080/10408360802485792
28. Zhang M., Liu B., Zhang Y., Wei H., Lei Y., Zhao L., Structural shifts of mucosa-associated lactobacilli and Clostridium leptum subgroup in patients with ulcerative colitis. Journal of Clinical Microbiology 2007 45 2 496 500 2-s2.0-33847045521 10.1128/JCM.01720-06
29. Nagalingam N. A., Lynch S. V., Role of the microbiota in inflammatory bowel diseases. Inflammatory Bowel Disease 2012 18 5 968 984 10.1002/ibd.21866
30. de Hertogh G., Geboes K., Crohn's disease and infections: a complex relationship. MedGenMed Medscape General Medicine 2004 6 3, article 14 2-s2.0-25144486717
31. Chiodini R. J., van Kruiningen H. J., Thayer R., Possible role of mycobacteria in inflammatory bowel disease. I. An unclassified Mycobacterium species isolated from patients with Crohn's disease. Digestive Diseases and Sciences 1984 29 12 1073 1079 2-s2.0-0021709791 (Pubitemid 15181471)
32. Bull T. J., McMinn E. J., Sidi-Boumedine K., Skull A., Durkin D., Neild P., Rhodes G., Pickup R., Hermon-Taylor J., Detection and verification of Mycobacterium avium subsp. paratuberculosis in fresh ileocolonic mucosal biopsy specimens from individuals with and without Crohn's disease. Journal of Clinical Microbiology 2003 41 7 2915 2923 2-s2.0-0038507158 10.1128/JCM.41.7.2915-2923. 2003 (Pubitemid 36842279)
33. Kirkwood C. D., Wagner J., Boniface K., Vaughan J., Michalski W. P., Catto-Smith A. G., Cameron D. J. S., Bishop R. F., Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease. Inflammatory Bowel Diseases 2009 15 11 1643 1655 2-s2.0-72549110084 10.1002/ibd.20967
34. Bernstein C. N., Wang M. H., Sargent M., Brant S. R., Collins M. T., Testing the interaction between NOD-2 status and serological response to Mycobacterium paratuberculosis in cases of inflammatory bowel disease. Journal of Clinical Microbiology 2007 45 3 968 971 2-s2.0-33947261744 10.1128/JCM.02062-06 (Pubitemid 46427719)
35. Collins M. D., Lawson P. A., Willems A., Cordoba J. J., Fernandez-Garayzabal J., Garcia P., Cai J., Hippe H., Farrow J. A. E., The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. International Journal of Systematic Bacteriology 1994 44 4 812 826 2-s2.0-0028126829 (Pubitemid 24315163)
36. Hampe J., Franke A., Rosenstiel P., Till A., Teuber M., Huse K., Albrecht M., Mayr G., de la Vega F. M., Briggs J., Günther S., Prescott N. J., Onnie C. M., Häsler R., Sipos B., Fölsch U. R., Lengauer T., Platzer M., Mathew C. G., Krawczak M., Schreiber S., A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nature Genetics 2007 39 2 207 211 2-s2.0-33846627302 10.1038/ng1954 (Pubitemid 46184351)
37. Duerr R. H., Taylor K. D., Brant S. R., Rioux J. D., Silverberg M. S., Daly M. J., Steinhart A. H., Abraham C., Regueiro M., Griffiths A., Dassopoulos T., Bitton A., Yang H., Targan S., Datta L. W., Kistner E. O., Schumm L. P., Lee A. T., Gregersen P. K., Barmada M. M., Rotter J. I., Nicolae D. L., Cho J. H., A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 2006 314 5804 1461 1463 2-s2.0-33845340501 10.1126/science.1135245 (Pubitemid 44871953)
38. Scharl M., Rogler G., Microbial sensing by the intestinal epithelium in the pathogenesis of inflammatory bowel disease. International Journal of Inflammation 2010 2010 12 671258 10.4061/2010/671258
39. Deretic V., Links between autophagy, innate immunity, inflammation and Crohn's disease. Digestive Diseases 2009 27 3 246 251 2-s2.0-70349924078 10.1159/000228557
40. Meconi S., Vercellone A., Levillain F., Payré B., Al Saati T., Capilla F., Desreumaux P., Darfeuille-michaud A., Altare F., Adherent-invasive Escherichia coli isolated from Crohn's disease patients induce granulomas in vitro. Cellular Microbiology 2007 9 5 1252 1261 2-s2.0-34047252362 10.1111/j.1462-5822.2006.00868.x (Pubitemid 46547142)
41. Biswas A., Petnicki-Ocwieja T., Kobayashi K. S., Nod2: a key regulator linking microbiota to intestinal mucosal immunity. Journal of Molecular Medicine 2012 90 1 15 24 10.1007/s00109-011-0802-y
42. Imielinski M., Baldassano R. N., Griffiths A., Common variants at five new loci associated with early-onset inflammatory bowel disease. Nature Genetics 2009 41 1335 1340 10.1038/ng.489
43. Eckburg P. B., Bik E. M., Bernstein C. N., Purdom E., Dethlefsen L., Sargent M., Gill S. R., Nelson K. E., Relman D. A., Microbiology: diversity of the human intestinal microbial flora. Science 2005 308 5728 1635 1638 2-s2.0-20544444045 10.1126/science.1110591 (Pubitemid 40807514)
44. Marks D. J. B., Defective innate immunity in inflammatory bowel disease: a Crohn's disease exclusivity? Current Opinion in Gastroenterology 2011 27 4 328 334 2-s2.0-79958774972 10.1097/MOG.0b013e3283463b45
45. Sewell G. W., Marks D. J., Segal A. W., The immunopathogenesis of Crohn's disease: a three-stage model. Current Opinion in Immunology 2009 21 5 506 513 2-s2.0-70349756909 10.1016/j.coi.2009.06.003
46. Frank D. N., Robertson C. E., Hamm C. M., Kpadeh Z., Zhang T., Chen H., Zhu W., Sartor R. B., Boedeker E. C., Harpaz N., Pace N. R., Li E., Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflammatory Bowel Diseases 2011 17 1 179 184 2-s2.0-78650099360 10.1002/ibd.21339
47. Frank D. N., Amand A. L. S., Feldman R. A., Boedeker E. C., Harpaz N., Pace N. R., Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences of the United States of America 2007 104 34 13780 13785 2-s2.0-35348857386 10.1073/pnas.0706625104 (Pubitemid 350003397)
48. Martinez-Medina M., Aldeguer X., Gonzalez-Huix F., Acero D., Garcia-Gil L. J., Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflammatory Bowel Diseases 2006 12 12 1136 1145 2-s2.0-33751556362 10.1097/01.mib.0000235828.09305.0c (Pubitemid 44847471)
49. Gilbert J. A., Meyer F., Jansson J., The Earth microbiome project: meeting report of the 1st EMP meeting on sample selection and acquisition at Argonne National Laboratory October 6th 2010. Standards in Genomic Sciences 2010 3 3 249 253 10.4056/aigs.1443528
50. Fava F., Danese S., Intestinal microbiota in inflammatory bowel disease: friend of foe? World Journal of Gastroenterology 2011 17 5 557 566 2-s2.0-79955935457 10.3748/wjg.v17.i5.557
51. Joossens M., Huys G., Cnockaert M., de Preter V., Verbeke K., Rutgeerts P., Vandamme P., Vermeire S., Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011 60 5 631 637 2-s2.0-79953748870 10.1136/gut.2010.223263
52. Seksik P., Rigottier-Gois L., Gramet G., Sutren M., Pochart P., Marteau P., Jian R., Doré J., Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 2003 52 2 237 242 2-s2.0-0037302961 10.1136/gut.52.2.237 (Pubitemid 36115065)
53. Scanlan P. D., Shanahan F., O'Mahony C., Marchesi J. R., Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease. Journal of Clinical Microbiology 2006 44 11 3980 3988 2-s2.0-33750932588 10.1128/JCM.00312-06 (Pubitemid 44737239)
54. Kang S., Denman S. E., Morrison M., Yu Z., Dore J., Leclerc M., McSweeney C. S., Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflammatory Bowel Diseases 2010 16 12 2034 2042 2-s2.0-78649622569 10.1002/ibd.21319
55. Michail S., Durbin M., Turner D., Alterations in the gut microbiome of children with severeulcerative colitis. Inflammatory Bowel Diseases. In press 10.1002/ibd.22860
56. Darfeuille-Michaud A., Boudeau J., Bulois P., Neut C., Glasser A. L., Barnich N., Bringer M. A., Swidsinski A., Beaugerie L., Colombel J. F., High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 2004 127 2 412 421 2-s2.0-4143069158 10.1053/j.gastro.2004.04.061 (Pubitemid 39091889)
57. Negroni A., Costanzo M., Vitali R., Characterization of adherent-invasive Escherichia coli isolated from pediatric patients with inflammatory bowel disease. Inflammatory Bowel Diseases 2012 18 5 913 924 10.1002/ibd.21899
58. Wehkamp J., Salzman N. H., Porter E., Reduced Paneth cell α -defensins in ileal Crohn's disease. Proceedings of the National Academy of Sciences of the United States of America 2005 102 50 18129 18134 10.1073/pnas.0505256102 (Pubitemid 41798513)
59. Nuding S., Fellermann K., Wehkamp J., Stange E. F., Reduced mucosal antimicrobial activity in Crohn's disease of the colon. Gut 2007 56 9 1240 1247 2-s2.0-34548130847 10.1136/gut.2006.118646 (Pubitemid 47300425)
60. Sartor R. B., Muehlbauer M., Microbial host interactions in IBD: implications for pathogenesis and therapy. Current Gastroenterology Reports 2007 9 6 497 507 2-s2.0-44249094435 10.1007/s11894-007-0066-4 (Pubitemid 351795708)
61. Gareau M. G., Sherman P. M., Walker W. A., Probiotics and the gut microbiota in intestinal health and disease. Nature Reviews. Gastroenterology & Hepatology 2010 7 9 503 514 2-s2.0-79952108387