Key questions to guide a better understanding of host-commensal microbiota interactions in intestinal inflammation

Mucosal Immunology

Volumn 4, Issue 2, 2011, Pages 127-132

  Sartor, R B ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; PROBIOTIC AGENT;

BACTERIAL COLONIZATION; BACTERIAL METABOLISM; COEVOLUTION; COMMENSAL; COMMENSALISM; CROHN DISEASE; DIETARY INTAKE; DRUG EFFECT; DRUG EFFICACY; EFFECTOR CELL; ENTERITIS; ENVIRONMENTAL EXPOSURE; FUNGAL STRAIN; GENETIC SUSCEPTIBILITY; GENOTYPE ENVIRONMENT INTERACTION; HOST PATHOGEN INTERACTION; HUMAN; IMMUNOREGULATION; IMMUNOSTIMULATION; INTESTINE FLORA; INTESTINE MUCOSA; METABOLITE; MICROBIAL ACTIVITY; MICROBIOME; NONHUMAN; PRIORITY JOURNAL; REVIEW; SPECIES COMPARISON; SPECIES COMPOSITION; TREATMENT PLANNING; VIRUS STRAIN;

EID: 79951868908     PISSN: 19330219     EISSN: None     Source Type: Journal    
DOI: 10.1038/mi.2010.87     Document Type: Review

References (68)

1. Hansen J Gulati A & Sartor R B The role of mucosal immunity and host genetics in defi ning intestinal commensal bacteria Curr Opin Gastroenterol 26 564 - 571 ( 2010 ).
2. Garrett W S Gordon J I & Glimcher L H Homeostasis and infl ammation in the intestine Cell 140 859 - 870 ( 2010 ).
3. Abraham C & Cho J H Infl ammatory bowel disease N Engl J Med 361 2066-2078 ( 2009 ).
4. Sartor R B Microbial influences in inflammatory bowel diseases Gastroenterology 134 577-594 (2008). (Pubitemid 351173057)
5. Vijay-Kumar M et al Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5 Science 328 228 - 231 ( 2010 ).
6. Nell S Suerbaum S & Josenhans C The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models Nat Rev Microbiol 8 564 - 577 ( 2010 ).
7. Purohit V et al Alcohol, intestinal bacterial growth, intestinal permeability to endotoxin, and medical consequences of a symposium Alcohol 42 349-361 ( 2008 ).
8. Xavier R J & Podolsky D K Unravelling the pathogenesis of infl ammatory bowel disease Nature 448 427-434 ( 2007 ). (Pubitemid 47123518)
9. Cadwell K et al Virus-plus-susceptibility gene interaction determines Crohns disease gene Atg16L1 phenotypes in intestine Cell 1411135 - 1145 ( 2010 ).
10. Frank D N et al Molecular-phylogenetic characterization of microbial community imbalances in human infl ammatory bowel diseases Proc Natl Acad Sci USA 104 13780-13785 ( 2007 ). (Pubitemid 350003397)
11. Darfeuille-Michaud A et al High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohns disease Gastroenterology 127 412-421 ( 2004 ). (Pubitemid 39091889)
12. Kotlowski R Bernstein C N Sepehri S & Krause D O High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in infl ammatory bowel disease Gut 56 669-675 ( 2007 ). (Pubitemid 46662933)
13. Baumgart M et al Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohns disease involving the ileum ISME J 1 403-418 ( 2007 ). (Pubitemid 47373247)
14. Patwa L G Sartor R B & Hansen J J Deletion of genes encoding E coli small heat shock proteins ibpA/B worsens experimental colitis in E coli monoassociated IL-10-defi cient mice Gastroenterology 138 ( 2010 ) (abstract).
15. Willing B et al A pyrosequencing study in twins shows that GI microbial profi les vary with infl ammatory bowel disease phenotypes Gastroenterology 139 1844 - 1854 ( 2010 ).
16. Garrett W S et al Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis Cell Host Microbe 8 292 - 300 ( 2010 ).
17. Sokol H et al Low counts of Faecalibacterium prausnitzii in colitis microbiota Infl amm Bowel Dis 15 1183-1189 ( 2009 ).
18. Sokol H et al Faecalibacterium prausnitzii is an antiinfl ammatory commensal bacterium identifi ed by gut microbiota analysis of Crohns disease patients Proc Natl Acad Sci USA 105 16731-16736 ( 2008 ).
19. Sellon R K et al Resident enteric bacteria are necessary for development of spontaneous colitis and immune system activation in interleukin-10-defi cient mice Infect Immun 66 5224-5231 ( 1998 ). (Pubitemid 29044613)
20. Kim S C et al Variable phenotypes of enterocolitis in interleukin 10-defi cient mice monoassociated with two different commensal bacteria Gastroenterology 128 891-906 ( 2005 ). (Pubitemid 40523542)
21. Ivanov I I et al Induction of intestinal Th17 cells by segmented fi lamentous bacteria Cell 139 485-498 ( 2009 ).
22. + T cells Infl amm Bowel Dis 13 1202-1211 ( 2007 ). (Pubitemid 47597767)
23. Moran J P Walter J Tannock G W Tonkonogy S L & Sartor R B Bifi dobacterium animalis causes extensive duodenitis and mild colonic infl ammation in monoassociated interleukin-10-defi cient mice Infl amm Bowel Dis 15 1022-1031 ( 2009 ).
24. Veiga P et al Bifi dobacterium animalis subsp lactis fermented milk product reduces infl ammation by altering a niche for colitogenic microbes Proc Natl Acad Sci USA 107 18132 - 18137 ( 2010 ).
25. Round J L & Mazmanian S K Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota Proc Natl Acad Sci USA 107 12204 - 12209 ( 2010 ).
26. Kim S C Tonkonogy S L Albright C A & Sartor R B Different host genetic backgrounds determine disease phenotypes induced by selective bacterial colonization Gastroenterology 128 A512 ( 2005 ).
27. Kim S C Tonkonogy S L Karrasch T Jobin C & Sartor R B Dual association of gnotobiotic IL-10-/- mice with two nonpathogenic commensal bacteria induces aggressive pancolitis Infl amm Bowel Dis 13 1457-1466 ( 2007 ).
28. Kim S C Tonkonogy S L Jarvis H W Darfeuille-Michaud A & Sartor R B Escherichia coli strains differentially induce colitis in IL-10 gene defi cient mice Gastroenterology 134 A23 ( 2008 ).
29. Garrett W S et al Communicable ulcerative colitis induced by T-bet defi ciency in the innate immune system Cell 131 33-45 (2007). (Pubitemid 47505255)
30. Simpson K W et al Adherent and invasive Escherichia coli is associated with granulomatous colitis in boxer dogs Infect Immun 74 4778-4792 ( 2006 ). (Pubitemid 44157265)
31. Suchodolski J S Xenoulis P G Paddock C G Steiner J M & Jergens A E Molecular analysis of the bacterial microbiota in duodenal biopsies from dogs with idiopathic infl ammatory bowel disease Vet Microbiol 142 394 - 400 ( 2010 ).
32. Petersen A M et al A phylogenetic group of Escherichia coli associated with active l eft-sided infl ammatory bowel disease BMC Microbiol 9 171 ( 2009 ).
33. Swidsinski A et al Mucosal fl ora in infl ammatory bowel disease Gastroenterology 122 44-54 ( 2002 ). (Pubitemid 34049193)
34. Hoffmann C et al Community-wide response of the gut microbiota to enteropathogenic Citrobacter rodentium infection revealed by deep sequencing Infect Immun 77 4668-4678 ( 2009 ).
35. Lupp C et al Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae Cell Host Microbe 2 119-129 ( 2007 ). (Pubitemid 47209521)
36. Costello E K et al Bacterial community variation in human body habitats across space and time Science 326 1694-1697 ( 2009 ).
37. Venturi A et al Impact on the composition of the faecal fl ora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis Aliment Pharmacol Ther 13 1103-1108 ( 1999 ). (Pubitemid 29374113)
38. Dethlefsen L & Relman D A Microbes and Health Sackler Colloquium: incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation Proc Natl Acad Sci USA e-pub ahead of print 16 September 2010.
39. Antonopoulos D A et al Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation Infect Immun 77 2367-2375 ( 2009 ).
40. Swidsinski A Loening-Baucke V Bengmark S Scholze J & Doerffel Y Bacterial biofi lm suppression with antibiotics for ulcerative and indeterminate colitis: consequences of aggressive treatment Arch Med Res 39 198-204 ( 2008 ).
41. Sartor R B Genetics and environmental interactions shape the intestinal microbiome to promote IBD vs mucosal homeostasis Gastroenterology 139 1816 - 1819 ( 2010 ).
42. Turnbaugh P J et al A core gut microbiome in obese and lean twins Nature 457 480-484 ( 2009 ).
43. Frank D N et al Clinical phenotype and genetic factors are associated with shifts in mucosal-associated microbiota in infl amatory bowel diseases Infl amm Bowel Dis 17 179 - 184 ( 2011 ).
44. Gulati A S Kruek L & Sartor R B Infl uence of NOD 2 on the protective intestinal commensal bacterium Faecalibacterium prausnitzii Gastroenterology 138 (Issue 5, Suppl 1) S-14 ( 2010 ).
45. Alexander D A et al Quantitative PCR assays for mouse enteric fl ora reveal strain-dependent differences in composition that are infl uenced by the microenvironment Mamm Genome 17 1093-1104 ( 2006 ).
46. Friswell M K et al Site and strain-specifi c variation in gut microbiota profi les and metabolism in experimental mice PLos One 5 e8584 ( 2010 ).
47. Adlerberth I & Wold A E Establishment of the gut microbiota in Western infants Acta Paediatr 98 229-238 ( 2009 ).
48. Vael C & Desager K The importance of the development of the intestinal microbiota in infancy Curr Opin Pediatr 21 794-800 ( 2009 ).
49. Dominguez-Bello M G et al Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns Proc Natl Acad Sci USA 107 11971 - 11975 ( 2010 ).
50. Palmer C Bik E M DiGiulio D B Relman D A & Brown P O Development of the human infant intestinal microbiota PLoS Biol 5 e177 ( 2007 ).
51. Penders J Stobberingh E E van den Brandt P A & Thijs C The role of the intestinal microbiota in the development of atopic disorders Allergy 62 1223-1236 ( 2007 ). (Pubitemid 47537504)
52. Osborn D A & Sinn J K Probiotics in infants for prevention of allergic disease and food hypersensitivity Cochrane Database Systematic Review Article number: CD006475 ( 2007 ).
53. Faith J J et al Creating and characterizing communities of human gut microbes in gnotobiotic mice ISME J 4 1094 - 1098 ( 2010 ).
54. Rhee K J et al Induction of persistent colitis by a human commensal, enterotoxigenic Bacteroides fragilis in wild-type C57BL/6 mice Infect Immun 77 1708-1718 ( 2009 ).
55. Gradel K O et al Increased short- and longterm risk of infl ammatory bowel disease after salmonella or campylobacter gastroenteritis Gastroenterology 137 495-501 ( 2009 ).
56. Jergens A E et al Helicobacter bilis triggers persistent immune reactivity to antigens derived from the commensal bacteria in gnotobiotic C3H/HeN mice Gut 56 934-940 ( 2007 ). (Pubitemid 46999076)
57. Onyeagocha C et al Latent cytomegalovirus infection exacerbates experimental colitis Am J Pathol 175 2034-2042 ( 2009 ).
58. Hormannsperger G & Haller D Molecular crosstalk of probiotic bacteria with the intestinal immune system: clinical relevance in the context of infl ammatory bowel disease Int J Med Microbiol 300 63 - 73 ( 2010 ).
59. Gulati A S & Dubinsky M C Probiotics in pediatric infl ammatory bowel diseases Curr Gastroenterol Rep 11 238-247 ( 2009 ).
60. Sonnenburg J L Chen C T & Gordon J I Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host PLoS Biol 4 e413 ( 2006 ).
61. Turnbaugh P J et al The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice Sci Transl Med 1 6ra14 ( 2009 ).
62. Sonnenburg J L et al Glycan foraging in vivo by an intestine-adapted bacterial symbiont Science 307 1955-1959 ( 2005 ). (Pubitemid 40404703)
63. Preidis G A & Versalovic J Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era Gastroenterology 136 2015-2031 ( 2009 ).
64. Quigley E M Prebiotics and probiotics; modifying and mining the microbiota Pharmacol Res 61 213 - 218 ( 2010 ).
65. Singh N et al Blockade of dendritic cell development by bacterial fermentation products butyrate and propionate through a transporter (Slc5a8)-dependent inhibition of histone deacetylases J Biol Chem 285 27601 - 27608 ( 2010 ).
66. Bailon E et al Butyrate in vitro immunemodulatory effects might be mediated through a proliferation-related induction of apoptosis Immunobiology 215 863 - 873 ( 2010 ).
67. Strus M et al Effect of hydrogen peroxide of bacterial origin on apoptosis and necrosis of gut mucosa epithelial cells as a possible pathomechanism of infl ammatory bowel disease and cancer J Physiol Pharmacol 60 (Suppl 6) 55-60 (2009).
68. Reyes A et al Viruses in the faecal microbiota of monozygotic twins and their mothers Nature 466 334-338 (2010)