Skip to main content
Top
Published in: Journal of Translational Medicine 1/2019

Open Access 01-12-2019 | Ulcerative Colitis | Review

Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine

Authors: Manoj Kumar, Mathieu Garand, Souhaila Al Khodor

Published in: Journal of Translational Medicine | Issue 1/2019

Login to get access

Abstract

Background

Inflammatory Bowel Disease (IBD) is a multifactorial chronic disease. Understanding only one aspect of IBD pathogenesis does not reflect the complex nature of IBD nor will it improve its clinical management. Therefore, it is vital to dissect the interactions between the different players in IBD pathogenesis in order to understand the biology of the disease and enhance its clinical outcomes.

Aims

To provide an overview of the available omics data used to assess the potential mechanisms through which various players are contributing to IBD pathogenesis and propose a precision medicine model to fill the current knowledge gap in IBD.

Results

Several studies have reported microbial dysbiosis, immune and metabolic dysregulation in IBD patients, however, this data is not sufficient to create signatures that can differentiate between the disease subtypes or between disease relapse and remission.

Conclusions

We summarized the current knowledge in the application of omics in IBD patients, and we showed that the current knowledge gap in IBD hinders the improvements of clinical decision for treatment as well as the prediction of disease relapse. We propose one way to fill this gap by implementing integrative analysis of various omics datasets generated from one patient at a single time point.
Literature
1.
go back to reference Mehta M, Ahmed S, Dryden G. Immunopathophysiology of inflammatory bowel disease: how genetics link barrier dysfunction and innate immunity to inflammation. Innate Immun. 2017;23:497–505.PubMedCrossRef Mehta M, Ahmed S, Dryden G. Immunopathophysiology of inflammatory bowel disease: how genetics link barrier dysfunction and innate immunity to inflammation. Innate Immun. 2017;23:497–505.PubMedCrossRef
3.
go back to reference Rieder F, Fiocchi C. Intestinal fibrosis in IBD—a dynamic, multifactorial process. Nat Rev Gastroenterol Hepatol. 2009;6:228–35.PubMedCrossRef Rieder F, Fiocchi C. Intestinal fibrosis in IBD—a dynamic, multifactorial process. Nat Rev Gastroenterol Hepatol. 2009;6:228–35.PubMedCrossRef
4.
go back to reference Yu YR, Rodriguez JR. Clinical presentation of Crohn’s, ulcerative colitis, and indeterminate colitis: symptoms, extraintestinal manifestations, and disease phenotypes. Semin Pediatr Surg. 2017;26:349–55.PubMedCrossRef Yu YR, Rodriguez JR. Clinical presentation of Crohn’s, ulcerative colitis, and indeterminate colitis: symptoms, extraintestinal manifestations, and disease phenotypes. Semin Pediatr Surg. 2017;26:349–55.PubMedCrossRef
5.
go back to reference Feakins RM. Ulcerative colitis or Crohn’s disease? Pitfalls and problems. Histopathology. 2014;64:317–35.PubMedCrossRef Feakins RM. Ulcerative colitis or Crohn’s disease? Pitfalls and problems. Histopathology. 2014;64:317–35.PubMedCrossRef
6.
go back to reference Tontini GE, Vecchi M, Pastorelli L, et al. Differential diagnosis in inflammatory bowel disease colitis: state of the art and future perspectives. World J Gastroenterol. 2015;21:21–46.PubMedPubMedCentralCrossRef Tontini GE, Vecchi M, Pastorelli L, et al. Differential diagnosis in inflammatory bowel disease colitis: state of the art and future perspectives. World J Gastroenterol. 2015;21:21–46.PubMedPubMedCentralCrossRef
7.
go back to reference Monteiro S, Dias de Castro F, Boal Carvalho P, et al. Essential role of small bowel capsule endoscopy in reclassification of colonic inflammatory bowel disease type unclassified. World J Gastrointest Endosc. 2017;9:34–40.PubMedPubMedCentralCrossRef Monteiro S, Dias de Castro F, Boal Carvalho P, et al. Essential role of small bowel capsule endoscopy in reclassification of colonic inflammatory bowel disease type unclassified. World J Gastrointest Endosc. 2017;9:34–40.PubMedPubMedCentralCrossRef
9.
go back to reference Samuel Wilks WM. Lectures on pathological anatomy: Lindsay and Blakiston. 1875. Samuel Wilks WM. Lectures on pathological anatomy: Lindsay and Blakiston. 1875.
11.
go back to reference Kim HJ, Hann HJ, Hong SN, et al. Incidence and natural course of inflammatory bowel disease in Korea, 2006–2012: a nationwide population-based study. Inflamm Bowel Dis. 2015;21:623–30.PubMedCrossRef Kim HJ, Hann HJ, Hong SN, et al. Incidence and natural course of inflammatory bowel disease in Korea, 2006–2012: a nationwide population-based study. Inflamm Bowel Dis. 2015;21:623–30.PubMedCrossRef
12.
go back to reference Molodecky NA, Soon IS, Rabi DM, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology. 2012;142:46–54.e42 (quiz e30).PubMedCrossRef Molodecky NA, Soon IS, Rabi DM, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology. 2012;142:46–54.e42 (quiz e30).PubMedCrossRef
13.
go back to reference Kaplan GG. The global burden of IBD: from 2015 to 2025. Nat Rev Gastroenterol Hepatol. 2015;12:720–7.PubMedCrossRef Kaplan GG. The global burden of IBD: from 2015 to 2025. Nat Rev Gastroenterol Hepatol. 2015;12:720–7.PubMedCrossRef
14.
go back to reference Sykora J, Pomahacova R, Kreslova M, et al. Current global trends in the incidence of pediatric-onset inflammatory bowel disease. World J Gastroenterol. 2018;24:2741–63.PubMedPubMedCentralCrossRef Sykora J, Pomahacova R, Kreslova M, et al. Current global trends in the incidence of pediatric-onset inflammatory bowel disease. World J Gastroenterol. 2018;24:2741–63.PubMedPubMedCentralCrossRef
15.
go back to reference Marchesi JR, Adams DH, Fava F, et al. The gut microbiota and host health: a new clinical frontier. Gut. 2016;65:330–9.PubMedCrossRef Marchesi JR, Adams DH, Fava F, et al. The gut microbiota and host health: a new clinical frontier. Gut. 2016;65:330–9.PubMedCrossRef
16.
go back to reference Imhann F, Vich Vila A, Bonder MJ, et al. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. 2018;67:108–19.PubMedCrossRef Imhann F, Vich Vila A, Bonder MJ, et al. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. 2018;67:108–19.PubMedCrossRef
17.
go back to reference Weersma RK, Xavier RJ, Consortium IBDMO, et al. Multiomics analyses to deliver the most effective treatment to every patient with inflammatory bowel disease. Gastroenterology. 2018;155:e1–4.PubMedCrossRef Weersma RK, Xavier RJ, Consortium IBDMO, et al. Multiomics analyses to deliver the most effective treatment to every patient with inflammatory bowel disease. Gastroenterology. 2018;155:e1–4.PubMedCrossRef
19.
go back to reference Levine A, Koletzko S, Turner D, et al. ESPGHAN revised porto criteria for the diagnosis of inflammatory bowel disease in children and adolescents. J Pediatr Gastroenterol Nutr. 2014;58:795–806.PubMed Levine A, Koletzko S, Turner D, et al. ESPGHAN revised porto criteria for the diagnosis of inflammatory bowel disease in children and adolescents. J Pediatr Gastroenterol Nutr. 2014;58:795–806.PubMed
20.
go back to reference Xu XR, Liu CQ, Feng BS, et al. Dysregulation of mucosal immune response in pathogenesis of inflammatory bowel disease. World J Gastroenterol. 2014;20:3255–64.PubMedPubMedCentralCrossRef Xu XR, Liu CQ, Feng BS, et al. Dysregulation of mucosal immune response in pathogenesis of inflammatory bowel disease. World J Gastroenterol. 2014;20:3255–64.PubMedPubMedCentralCrossRef
23.
go back to reference Tharian B, George N, Navaneethan U. Endoscopy in the diagnosis and management of complications of inflammatory bowel disease. Inflamm Bowel Dis. 2016;22:1184–97.PubMedCrossRef Tharian B, George N, Navaneethan U. Endoscopy in the diagnosis and management of complications of inflammatory bowel disease. Inflamm Bowel Dis. 2016;22:1184–97.PubMedCrossRef
24.
go back to reference Taylor S, Lobo AJ. Diagnosis and treatment of inflammatory bowel disease. Practitioner. 2016;260:19–23.PubMed Taylor S, Lobo AJ. Diagnosis and treatment of inflammatory bowel disease. Practitioner. 2016;260:19–23.PubMed
25.
go back to reference Padoan A, D’Inca R, Scapellato ML, et al. Improving IBD diagnosis and monitoring by understanding preanalytical, analytical and biological fecal calprotectin variability. Clin Chem Lab Med. 2018;56:1926–35.PubMedCrossRef Padoan A, D’Inca R, Scapellato ML, et al. Improving IBD diagnosis and monitoring by understanding preanalytical, analytical and biological fecal calprotectin variability. Clin Chem Lab Med. 2018;56:1926–35.PubMedCrossRef
26.
go back to reference Koksal AR, Boga S, Alkim H, et al. How does a biopsy of endoscopically normal terminal ileum contribute to the diagnosis? Which patients should undergo biopsy? Libyan J Med. 2014;9:23441.PubMedCrossRef Koksal AR, Boga S, Alkim H, et al. How does a biopsy of endoscopically normal terminal ileum contribute to the diagnosis? Which patients should undergo biopsy? Libyan J Med. 2014;9:23441.PubMedCrossRef
27.
go back to reference Magro F, Langner C, Driessen A, et al. European consensus on the histopathology of inflammatory bowel disease. J Crohns Colitis. 2013;7:827–51.PubMedCrossRef Magro F, Langner C, Driessen A, et al. European consensus on the histopathology of inflammatory bowel disease. J Crohns Colitis. 2013;7:827–51.PubMedCrossRef
28.
go back to reference Surawicz CM, Haggitt RC, Husseman M, et al. Mucosal biopsy diagnosis of colitis: acute self-limited colitis and idiopathic inflammatory bowel disease. Gastroenterology. 1994;107:755–63.PubMedCrossRef Surawicz CM, Haggitt RC, Husseman M, et al. Mucosal biopsy diagnosis of colitis: acute self-limited colitis and idiopathic inflammatory bowel disease. Gastroenterology. 1994;107:755–63.PubMedCrossRef
29.
go back to reference Levine A, Griffiths A, Markowitz J, et al. Pediatric modification of the Montreal classification for inflammatory bowel disease: the Paris classification. Inflamm Bowel Dis. 2011;17:1314–21.PubMedCrossRef Levine A, Griffiths A, Markowitz J, et al. Pediatric modification of the Montreal classification for inflammatory bowel disease: the Paris classification. Inflamm Bowel Dis. 2011;17:1314–21.PubMedCrossRef
30.
go back to reference Kornbluth A, Sachar DB, Practice Parameters Committee of the American College of G. Ulcerative colitis practice guidelines in adults (update): American College of Gastroenterology, Practice Parameters Committee. Am J Gastroenterol. 2004;99:1371–85.PubMedCrossRef Kornbluth A, Sachar DB, Practice Parameters Committee of the American College of G. Ulcerative colitis practice guidelines in adults (update): American College of Gastroenterology, Practice Parameters Committee. Am J Gastroenterol. 2004;99:1371–85.PubMedCrossRef
31.
go back to reference Lichtenstein GR, Loftus EV, Isaacs KL, et al. ACG clinical guideline: management of Crohn’s disease in adults. Am J Gastroenterol. 2018;113:481–517.PubMedCrossRef Lichtenstein GR, Loftus EV, Isaacs KL, et al. ACG clinical guideline: management of Crohn’s disease in adults. Am J Gastroenterol. 2018;113:481–517.PubMedCrossRef
32.
go back to reference Bartunkova J, Kolarova I, Sediva A, et al. Antineutrophil cytoplasmic antibodies, anti-Saccharomyces cerevisiae antibodies, and specific IgE to food allergens in children with inflammatory bowel diseases. Clin Immunol. 2002;102:162–8.PubMedCrossRef Bartunkova J, Kolarova I, Sediva A, et al. Antineutrophil cytoplasmic antibodies, anti-Saccharomyces cerevisiae antibodies, and specific IgE to food allergens in children with inflammatory bowel diseases. Clin Immunol. 2002;102:162–8.PubMedCrossRef
33.
go back to reference Matsui T, Yao T, Sakurai T, et al. Clinical features and pattern of indeterminate colitis: Crohn’s disease with ulcerative colitis-like clinical presentation. J Gastroenterol. 2003;38:647–55.PubMedCrossRef Matsui T, Yao T, Sakurai T, et al. Clinical features and pattern of indeterminate colitis: Crohn’s disease with ulcerative colitis-like clinical presentation. J Gastroenterol. 2003;38:647–55.PubMedCrossRef
34.
go back to reference Franke A, McGovern DP, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nat Genet. 2010;42:1118–25.PubMedPubMedCentralCrossRef Franke A, McGovern DP, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nat Genet. 2010;42:1118–25.PubMedPubMedCentralCrossRef
36.
go back to reference Shaw KA, Cutler DJ, Okou D, et al. Genetic variants and pathways implicated in a pediatric inflammatory bowel disease cohort. Genes Immun. 2019;20:131–42.PubMedCrossRef Shaw KA, Cutler DJ, Okou D, et al. Genetic variants and pathways implicated in a pediatric inflammatory bowel disease cohort. Genes Immun. 2019;20:131–42.PubMedCrossRef
37.
go back to reference Homer CR, Richmond AL, Rebert NA, et al. ATG16L1 and NOD2 interact in an autophagy-dependent antibacterial pathway implicated in Crohn’s disease pathogenesis. Gastroenterology. 2010;139:1630–41, 1641 e1–2.CrossRef Homer CR, Richmond AL, Rebert NA, et al. ATG16L1 and NOD2 interact in an autophagy-dependent antibacterial pathway implicated in Crohn’s disease pathogenesis. Gastroenterology. 2010;139:1630–41, 1641 e1–2.CrossRef
38.
go back to reference Wellcome Trust Case Control C. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661–78.CrossRef Wellcome Trust Case Control C. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661–78.CrossRef
40.
go back to reference Althani AA, Marei HE, Hamdi WS, et al. Human microbiome and its association with health and diseases. J Cell Physiol. 2016;231:1688–94.PubMedCrossRef Althani AA, Marei HE, Hamdi WS, et al. Human microbiome and its association with health and diseases. J Cell Physiol. 2016;231:1688–94.PubMedCrossRef
41.
go back to reference Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.CrossRef Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.CrossRef
42.
go back to reference Singh P, Kumar M, Al Khodor S. Vitamin D deficiency in the gulf cooperation council: exploring the triad of genetic predisposition, the gut microbiome and the immune system. Front Immunol. 2019;10:1042.PubMedPubMedCentralCrossRef Singh P, Kumar M, Al Khodor S. Vitamin D deficiency in the gulf cooperation council: exploring the triad of genetic predisposition, the gut microbiome and the immune system. Front Immunol. 2019;10:1042.PubMedPubMedCentralCrossRef
44.
go back to reference Lederberg J, McCray AT. ‘Ome Sweet’ omics—a genealogical treasury of words. Scientist. 2001;15:8. Lederberg J, McCray AT. ‘Ome Sweet’ omics—a genealogical treasury of words. Scientist. 2001;15:8.
45.
go back to reference Gupta VK, Paul S, Dutta C. Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol. 2017;8:1162.PubMedPubMedCentralCrossRef Gupta VK, Paul S, Dutta C. Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol. 2017;8:1162.PubMedPubMedCentralCrossRef
46.
go back to reference Barko PC, McMichael MA, Swanson KS, et al. The gastrointestinal microbiome: a review. J Vet Intern Med. 2018;32:9–25.PubMedCrossRef Barko PC, McMichael MA, Swanson KS, et al. The gastrointestinal microbiome: a review. J Vet Intern Med. 2018;32:9–25.PubMedCrossRef
47.
48.
go back to reference Hoffmann C, Dollive S, Grunberg S, et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE. 2013;8:e66019.PubMedPubMedCentralCrossRef Hoffmann C, Dollive S, Grunberg S, et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE. 2013;8:e66019.PubMedPubMedCentralCrossRef
51.
go back to reference Sirisinha S. The potential impact of gut microbiota on your health: current status and future challenges. Asian Pac J Allergy Immunol. 2016;34:249–64.PubMed Sirisinha S. The potential impact of gut microbiota on your health: current status and future challenges. Asian Pac J Allergy Immunol. 2016;34:249–64.PubMed
52.
go back to reference Weiss GA, Hennet T. Mechanisms and consequences of intestinal dysbiosis. Cell Mol Life Sci. 2017;74:2959–77.PubMedCrossRef Weiss GA, Hennet T. Mechanisms and consequences of intestinal dysbiosis. Cell Mol Life Sci. 2017;74:2959–77.PubMedCrossRef
53.
go back to reference Peng J, Xiao X, Hu M, et al. Interaction between gut microbiome and cardiovascular disease. Life Sci. 2018;214:153–7.PubMedCrossRef Peng J, Xiao X, Hu M, et al. Interaction between gut microbiome and cardiovascular disease. Life Sci. 2018;214:153–7.PubMedCrossRef
54.
go back to reference Mangiola F, Nicoletti A, Gasbarrini A, et al. Gut microbiota and aging. Eur Rev Med Pharmacol Sci. 2018;22:7404–13.PubMed Mangiola F, Nicoletti A, Gasbarrini A, et al. Gut microbiota and aging. Eur Rev Med Pharmacol Sci. 2018;22:7404–13.PubMed
55.
go back to reference Liu J, Wu M, He J, et al. Antibiotic-induced dysbiosis of gut microbiota impairs corneal nerve regeneration by affecting CCR2-negative macrophage distribution. Am J Pathol. 2018;188:2786–99.PubMedPubMedCentralCrossRef Liu J, Wu M, He J, et al. Antibiotic-induced dysbiosis of gut microbiota impairs corneal nerve regeneration by affecting CCR2-negative macrophage distribution. Am J Pathol. 2018;188:2786–99.PubMedPubMedCentralCrossRef
56.
go back to reference Li N, Wang Q, Wang Y, et al. Oral probiotics ameliorate the behavioral deficits induced by chronic mild stress in mice via the gut microbiota-inflammation axis. Front Behav Neurosci. 2018;12:266.PubMedPubMedCentralCrossRef Li N, Wang Q, Wang Y, et al. Oral probiotics ameliorate the behavioral deficits induced by chronic mild stress in mice via the gut microbiota-inflammation axis. Front Behav Neurosci. 2018;12:266.PubMedPubMedCentralCrossRef
58.
go back to reference Joossens M, Faust K, Gryp T, et al. Gut microbiota dynamics and uraemic toxins: one size does not fit all. Gut. 2019;68:2257–60.PubMedCrossRef Joossens M, Faust K, Gryp T, et al. Gut microbiota dynamics and uraemic toxins: one size does not fit all. Gut. 2019;68:2257–60.PubMedCrossRef
59.
go back to reference Bell JS, Spencer JI, Yates RL, et al. From nose to gut—the role of the microbiome in neurological disease. Neuropathol Appl Neurobiol. 2018. Bell JS, Spencer JI, Yates RL, et al. From nose to gut—the role of the microbiome in neurological disease. Neuropathol Appl Neurobiol. 2018.
61.
go back to reference Dickson I. Gut microbiota: diagnosing IBD with the gut microbiome. Nat Rev Gastroenterol Hepatol. 2017;14:195.PubMedCrossRef Dickson I. Gut microbiota: diagnosing IBD with the gut microbiome. Nat Rev Gastroenterol Hepatol. 2017;14:195.PubMedCrossRef
62.
go back to reference Flint HJ, Scott KP, Louis P, et al. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol. 2012;9:577–89.PubMedCrossRef Flint HJ, Scott KP, Louis P, et al. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol. 2012;9:577–89.PubMedCrossRef
63.
go back to reference Al Khodor S, Shatat IF. Gut microbiome and kidney disease: a bidirectional relationship. Pediatr Nephrol. 2017;32:921–31.PubMedCrossRef Al Khodor S, Shatat IF. Gut microbiome and kidney disease: a bidirectional relationship. Pediatr Nephrol. 2017;32:921–31.PubMedCrossRef
64.
66.
go back to reference Qin Y, Roberts JD, Grimm SA, et al. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression. Genome Biol. 2018;19:7.PubMedPubMedCentralCrossRef Qin Y, Roberts JD, Grimm SA, et al. An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression. Genome Biol. 2018;19:7.PubMedPubMedCentralCrossRef
67.
go back to reference Murugesan S, Nirmalkar K, Hoyo-Vadillo C, et al. Gut microbiome production of short-chain fatty acids and obesity in children. Eur J Clin Microbiol Infect Dis. 2018;37:621–5.PubMedCrossRef Murugesan S, Nirmalkar K, Hoyo-Vadillo C, et al. Gut microbiome production of short-chain fatty acids and obesity in children. Eur J Clin Microbiol Infect Dis. 2018;37:621–5.PubMedCrossRef
68.
go back to reference Luo Y, Blackledge WC. Microbiome-based mechanisms hypothesized to initiate obesity-associated rheumatoid arthritis. Obes Rev. 2018;19:786–97.PubMedCrossRef Luo Y, Blackledge WC. Microbiome-based mechanisms hypothesized to initiate obesity-associated rheumatoid arthritis. Obes Rev. 2018;19:786–97.PubMedCrossRef
69.
go back to reference Leong KSW, Derraik JGB, Hofman PL, et al. Antibiotics, gut microbiome and obesity. Clin Endocrinol. 2018;88:185–200.CrossRef Leong KSW, Derraik JGB, Hofman PL, et al. Antibiotics, gut microbiome and obesity. Clin Endocrinol. 2018;88:185–200.CrossRef
70.
go back to reference Langan EA, Gratz V, Billmann F, et al. Does the gastrointestinal microbiome contribute to the ‘obesity paradox’ in melanoma survival? Br J Dermatol. 2018;179:225–6.PubMedCrossRef Langan EA, Gratz V, Billmann F, et al. Does the gastrointestinal microbiome contribute to the ‘obesity paradox’ in melanoma survival? Br J Dermatol. 2018;179:225–6.PubMedCrossRef
71.
go back to reference Cheng M, Zhang X, Zhu J, et al. A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols. Food Funct. 2018;9:1079–87.PubMedCrossRef Cheng M, Zhang X, Zhu J, et al. A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols. Food Funct. 2018;9:1079–87.PubMedCrossRef
72.
go back to reference Castaner O, Goday A, Park YM, et al. The gut microbiome profile in obesity: a systematic review. Int J Endocrinol. 2018;2018:4095789.PubMedPubMedCentral Castaner O, Goday A, Park YM, et al. The gut microbiome profile in obesity: a systematic review. Int J Endocrinol. 2018;2018:4095789.PubMedPubMedCentral
73.
go back to reference Fedorak RN, Ismond KP. Practical considerations and the intestinal microbiome in disease: antibiotics for IBD therapy. Dig Dis. 2016;34:112–21.PubMedCrossRef Fedorak RN, Ismond KP. Practical considerations and the intestinal microbiome in disease: antibiotics for IBD therapy. Dig Dis. 2016;34:112–21.PubMedCrossRef
74.
go back to reference Hansen JJ, Sartor RB. Therapeutic manipulation of the microbiome in IBD: current results and future approaches. Curr Treat Options Gastroenterol. 2015;13:105–20.PubMedPubMedCentralCrossRef Hansen JJ, Sartor RB. Therapeutic manipulation of the microbiome in IBD: current results and future approaches. Curr Treat Options Gastroenterol. 2015;13:105–20.PubMedPubMedCentralCrossRef
75.
go back to reference Lavelle A, Sokol H. Gut microbiota: beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD. Nat Rev Gastroenterol Hepatol. 2018;15:193–4.PubMedCrossRef Lavelle A, Sokol H. Gut microbiota: beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD. Nat Rev Gastroenterol Hepatol. 2018;15:193–4.PubMedCrossRef
76.
go back to reference Rehman A, Rausch P, Wang J, et al. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut. 2016;65:238–48.PubMedCrossRef Rehman A, Rausch P, Wang J, et al. Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut. 2016;65:238–48.PubMedCrossRef
77.
go back to reference Santoru ML, Piras C, Murgia A, et al. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci Rep. 2017;7:9523.PubMedPubMedCentralCrossRef Santoru ML, Piras C, Murgia A, et al. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci Rep. 2017;7:9523.PubMedPubMedCentralCrossRef
78.
go back to reference Sitkin S, Vakhitov T, Pokrotnieks J. How to increase the butyrate-producing capacity of the gut microbiome: do IBD patients really need butyrate replacement and butyrogenic therapy? J Crohns Colitis. 2018;12:881–2.PubMedCrossRef Sitkin S, Vakhitov T, Pokrotnieks J. How to increase the butyrate-producing capacity of the gut microbiome: do IBD patients really need butyrate replacement and butyrogenic therapy? J Crohns Colitis. 2018;12:881–2.PubMedCrossRef
79.
go back to reference Wu GD. Diet, the gut microbiome and the metabolome in IBD. Nestle Nutr Inst Workshop Ser. 2014;79:73–82.PubMedCrossRef Wu GD. Diet, the gut microbiome and the metabolome in IBD. Nestle Nutr Inst Workshop Ser. 2014;79:73–82.PubMedCrossRef
80.
go back to reference Kumar M, Mathur T, Joshi V, et al. Effect of DS-2969b, a novel GyrB inhibitor, on rat and monkey intestinal microbiota. Anaerobe. 2018;51:120–3.PubMedCrossRef Kumar M, Mathur T, Joshi V, et al. Effect of DS-2969b, a novel GyrB inhibitor, on rat and monkey intestinal microbiota. Anaerobe. 2018;51:120–3.PubMedCrossRef
81.
go back to reference Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: an update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol. 2014;5:213–27.PubMedPubMedCentralCrossRef Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: an update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol. 2014;5:213–27.PubMedPubMedCentralCrossRef
82.
go back to reference Lopez-Siles M, Martinez-Medina M, Busquets D, et al. Mucosa-associated Faecalibacterium prausnitzii and Escherichia coli co-abundance can distinguish Irritable Bowel Syndrome and Inflammatory Bowel Disease phenotypes. Int J Med Microbiol. 2014;304:464–75.PubMedCrossRef Lopez-Siles M, Martinez-Medina M, Busquets D, et al. Mucosa-associated Faecalibacterium prausnitzii and Escherichia coli co-abundance can distinguish Irritable Bowel Syndrome and Inflammatory Bowel Disease phenotypes. Int J Med Microbiol. 2014;304:464–75.PubMedCrossRef
83.
go back to reference Takahashi K, Nishida A, Fujimoto T, et al. Reduced abundance of butyrate-producing bacteria species in the fecal microbial community in Crohn’s disease. Digestion. 2016;93:59–65.CrossRefPubMed Takahashi K, Nishida A, Fujimoto T, et al. Reduced abundance of butyrate-producing bacteria species in the fecal microbial community in Crohn’s disease. Digestion. 2016;93:59–65.CrossRefPubMed
84.
go back to reference 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;63:1275–83.CrossRefPubMed 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;63:1275–83.CrossRefPubMed
85.
go back to reference Willing BP, Dicksved J, Halfvarson J, et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology. 2010;139(1844–1854):e1. Willing BP, Dicksved J, Halfvarson J, et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology. 2010;139(1844–1854):e1.
86.
go back to reference Conte MP, Longhi C, Marazzato M, et al. Adherent-invasive Escherichia coli (AIEC) in pediatric Crohn’s disease patients: phenotypic and genetic pathogenic features. BMC Res Notes. 2014;7:748.PubMedPubMedCentralCrossRef Conte MP, Longhi C, Marazzato M, et al. Adherent-invasive Escherichia coli (AIEC) in pediatric Crohn’s disease patients: phenotypic and genetic pathogenic features. BMC Res Notes. 2014;7:748.PubMedPubMedCentralCrossRef
87.
go back to reference Man SM, Zhang L, Day AS, et al. Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn’s disease. Inflamm Bowel Dis. 2010;16:1008–16.PubMedCrossRef Man SM, Zhang L, Day AS, et al. Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn’s disease. Inflamm Bowel Dis. 2010;16:1008–16.PubMedCrossRef
88.
go back to reference Rowan F, Docherty NG, Murphy M, et al. Desulfovibrio bacterial species are increased in ulcerative colitis. Dis Colon Rectum. 2010;53:1530–6.PubMedCrossRef Rowan F, Docherty NG, Murphy M, et al. Desulfovibrio bacterial species are increased in ulcerative colitis. Dis Colon Rectum. 2010;53:1530–6.PubMedCrossRef
89.
go back to reference Negroni A, Costanzo M, Vitali R, et al. Characterization of adherent-invasive Escherichia coli isolated from pediatric patients with inflammatory bowel disease. Inflamm Bowel Dis. 2012;18:913–24.PubMedCrossRef Negroni A, Costanzo M, Vitali R, et al. Characterization of adherent-invasive Escherichia coli isolated from pediatric patients with inflammatory bowel disease. Inflamm Bowel Dis. 2012;18:913–24.PubMedCrossRef
90.
go back to reference Campos N, Magro F, Castro AR, et al. Macrophages from IBD patients exhibit defective tumour necrosis factor-alpha secretion but otherwise normal or augmented pro-inflammatory responses to infection. Immunobiology. 2011;216:961–70.PubMedCrossRef Campos N, Magro F, Castro AR, et al. Macrophages from IBD patients exhibit defective tumour necrosis factor-alpha secretion but otherwise normal or augmented pro-inflammatory responses to infection. Immunobiology. 2011;216:961–70.PubMedCrossRef
91.
go back to reference Sasaki M, Sitaraman SV, Babbin BA, et al. Invasive Escherichia coli are a feature of Crohn’s disease. Lab Investig. 2007;87:1042–54.PubMedCrossRef Sasaki M, Sitaraman SV, Babbin BA, et al. Invasive Escherichia coli are a feature of Crohn’s disease. Lab Investig. 2007;87:1042–54.PubMedCrossRef
92.
go back to reference Zhang S, Fu J, Dogan B, et al. 5-Aminosalicylic acid downregulates the growth and virulence of Escherichia coli associated with IBD and colorectal cancer, and upregulates host anti-inflammatory activity. J Antibiot. 2018;71:950–61.CrossRef Zhang S, Fu J, Dogan B, et al. 5-Aminosalicylic acid downregulates the growth and virulence of Escherichia coli associated with IBD and colorectal cancer, and upregulates host anti-inflammatory activity. J Antibiot. 2018;71:950–61.CrossRef
93.
go back to reference Renouf MJ, Cho YH, McPhee JB. Emergent behavior of IBD-associated Escherichia coli during disease. Inflamm Bowel Dis. 2019;25(1):33–44.PubMedCrossRef Renouf MJ, Cho YH, McPhee JB. Emergent behavior of IBD-associated Escherichia coli during disease. Inflamm Bowel Dis. 2019;25(1):33–44.PubMedCrossRef
94.
go back to reference Ummarino D. Spondyloarthropathies: E. coli links IBD to spondyloarthritis. Nat Rev Rheumatol. 2017;13:198.PubMedCrossRef Ummarino D. Spondyloarthropathies: E. coli links IBD to spondyloarthritis. Nat Rev Rheumatol. 2017;13:198.PubMedCrossRef
95.
go back to reference Kotlowski R. Use of Escherichia coli Nissle 1917 producing recombinant colicins for treatment of IBD patients. Med Hypotheses. 2016;93:8–10.PubMedCrossRef Kotlowski R. Use of Escherichia coli Nissle 1917 producing recombinant colicins for treatment of IBD patients. Med Hypotheses. 2016;93:8–10.PubMedCrossRef
96.
go back to reference Bucker R, Schulz E, Gunzel D, et al. alpha-Haemolysin of Escherichia coli in IBD: a potentiator of inflammatory activity in the colon. Gut. 2014;63:1893–901.PubMedCrossRef Bucker R, Schulz E, Gunzel D, et al. alpha-Haemolysin of Escherichia coli in IBD: a potentiator of inflammatory activity in the colon. Gut. 2014;63:1893–901.PubMedCrossRef
97.
go back to reference Ray K. IBD: fertilizing the gut: host-derived nitrate contributes to Escherichia coli bloom in colitis. Nat Rev Gastroenterol Hepatol. 2013;10:197.PubMedCrossRef Ray K. IBD: fertilizing the gut: host-derived nitrate contributes to Escherichia coli bloom in colitis. Nat Rev Gastroenterol Hepatol. 2013;10:197.PubMedCrossRef
98.
go back to reference Darfeuille-Michaud A, Colombel JF. Pathogenic Escherichia coli in inflammatory bowel diseases: proceedings of the 1st international meeting on E. coli and IBD, June 2007, Lille, France. J Crohns Colitis. 2008;2:255–62.PubMedCrossRef Darfeuille-Michaud A, Colombel JF. Pathogenic Escherichia coli in inflammatory bowel diseases: proceedings of the 1st international meeting on E. coli and IBD, June 2007, Lille, France. J Crohns Colitis. 2008;2:255–62.PubMedCrossRef
99.
go back to reference La Ferla K, Seegert D, Schreiber S. Activation of NF-kappaB in intestinal epithelial cells by E. coli strains isolated from the colonic mucosa of IBD patients. Int J Colorectal Dis. 2004;19:334–42.PubMedCrossRef La Ferla K, Seegert D, Schreiber S. Activation of NF-kappaB in intestinal epithelial cells by E. coli strains isolated from the colonic mucosa of IBD patients. Int J Colorectal Dis. 2004;19:334–42.PubMedCrossRef
100.
go back to reference O’Brien CL, Bringer MA, Holt KE, et al. Comparative genomics of Crohn’s disease-associated adherent-invasive Escherichia coli. Gut. 2017;66:1382–9.PubMedCrossRef O’Brien CL, Bringer MA, Holt KE, et al. Comparative genomics of Crohn’s disease-associated adherent-invasive Escherichia coli. Gut. 2017;66:1382–9.PubMedCrossRef
101.
go back to reference Zhang Y, Rowehl L, Krumsiek JM, et al. Identification of candidate adherent-invasive E. coli signature transcripts by genomic/transcriptomic analysis. PLoS ONE. 2015;10:e0130902.PubMedPubMedCentralCrossRef Zhang Y, Rowehl L, Krumsiek JM, et al. Identification of candidate adherent-invasive E. coli signature transcripts by genomic/transcriptomic analysis. PLoS ONE. 2015;10:e0130902.PubMedPubMedCentralCrossRef
102.
go back to reference Borruel N, Carol M, Casellas F, et al. Increased mucosal tumour necrosis factor alpha production in Crohn’s disease can be downregulated ex vivo by probiotic bacteria. Gut. 2002;51:659–64.PubMedPubMedCentralCrossRef Borruel N, Carol M, Casellas F, et al. Increased mucosal tumour necrosis factor alpha production in Crohn’s disease can be downregulated ex vivo by probiotic bacteria. Gut. 2002;51:659–64.PubMedPubMedCentralCrossRef
103.
go back to reference Glasser AL, Boudeau J, Barnich N, et al. Adherent invasive Escherichia coli strains from patients with Crohn’s disease survive and replicate within macrophages without inducing host cell death. Infect Immun. 2001;69:5529–37.PubMedPubMedCentralCrossRef Glasser AL, Boudeau J, Barnich N, et al. Adherent invasive Escherichia coli strains from patients with Crohn’s disease survive and replicate within macrophages without inducing host cell death. Infect Immun. 2001;69:5529–37.PubMedPubMedCentralCrossRef
104.
go back to reference Wagner J, Short K, Catto-Smith AG, et al. Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn’s disease. PLoS ONE. 2008;3:e3578.PubMedPubMedCentralCrossRef Wagner J, Short K, Catto-Smith AG, et al. Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn’s disease. PLoS ONE. 2008;3:e3578.PubMedPubMedCentralCrossRef
105.
go back to reference Wei B, Huang T, Dalwadi H, et al. Pseudomonas fluorescens encodes the Crohn’s disease-associated I2 sequence and T-cell superantigen. Infect Immun. 2002;70:6567–75.PubMedPubMedCentralCrossRef Wei B, Huang T, Dalwadi H, et al. Pseudomonas fluorescens encodes the Crohn’s disease-associated I2 sequence and T-cell superantigen. Infect Immun. 2002;70:6567–75.PubMedPubMedCentralCrossRef
106.
go back to reference Horing E, Gopfert D, Schroter G, et al. Frequency and spectrum of microorganisms isolated from biopsy specimens in chronic colitis. Endoscopy. 1991;23:325–7.PubMedCrossRef Horing E, Gopfert D, Schroter G, et al. Frequency and spectrum of microorganisms isolated from biopsy specimens in chronic colitis. Endoscopy. 1991;23:325–7.PubMedCrossRef
107.
go back to reference Mottawea W, Chiang CK, Muhlbauer M, et al. Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn’s disease. Nat Commun. 2016;7:13419.PubMedPubMedCentralCrossRef Mottawea W, Chiang CK, Muhlbauer M, et al. Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn’s disease. Nat Commun. 2016;7:13419.PubMedPubMedCentralCrossRef
108.
go back to reference Bashir A, Miskeen AY, Hazari YM, et al. Fusobacterium nucleatum, inflammation, and immunity: the fire within human gut. Tumour Biol. 2016;37:2805–10.PubMedCrossRef Bashir A, Miskeen AY, Hazari YM, et al. Fusobacterium nucleatum, inflammation, and immunity: the fire within human gut. Tumour Biol. 2016;37:2805–10.PubMedCrossRef
109.
go back to reference Strauss J, Kaplan GG, Beck PL, et al. Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis. 2011;17:1971–8.PubMedCrossRef Strauss J, Kaplan GG, Beck PL, et al. Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis. 2011;17:1971–8.PubMedCrossRef
110.
111.
go back to reference Alipour M, Zaidi D, Valcheva R, et al. Mucosal barrier depletion and loss of bacterial diversity are primary abnormalities in paediatric ulcerative colitis. J Crohns Colitis. 2016;10:462–71.PubMedCrossRef Alipour M, Zaidi D, Valcheva R, et al. Mucosal barrier depletion and loss of bacterial diversity are primary abnormalities in paediatric ulcerative colitis. J Crohns Colitis. 2016;10:462–71.PubMedCrossRef
112.
go back to reference Cader MZ, Kaser A. Recent advances in inflammatory bowel disease: mucosal immune cells in intestinal inflammation. Gut. 2013;62:1653–64.PubMedCrossRef Cader MZ, Kaser A. Recent advances in inflammatory bowel disease: mucosal immune cells in intestinal inflammation. Gut. 2013;62:1653–64.PubMedCrossRef
113.
go back to reference Gordon HA. Morphological and physiological characterization of germfree life. Ann N Y Acad Sci. 1959;78:208–20.PubMedCrossRef Gordon HA. Morphological and physiological characterization of germfree life. Ann N Y Acad Sci. 1959;78:208–20.PubMedCrossRef
114.
115.
go back to reference Martini E, Krug SM, Siegmund B, et al. Mend your fences: the epithelial barrier and its relationship with mucosal immunity in inflammatory bowel disease. Cell Mol Gastroenterol Hepatol. 2017;4:33–46.PubMedPubMedCentralCrossRef Martini E, Krug SM, Siegmund B, et al. Mend your fences: the epithelial barrier and its relationship with mucosal immunity in inflammatory bowel disease. Cell Mol Gastroenterol Hepatol. 2017;4:33–46.PubMedPubMedCentralCrossRef
116.
go back to reference Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119–24.PubMedPubMedCentralCrossRef Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119–24.PubMedPubMedCentralCrossRef
117.
go back to reference Kang S, Denman SE, Morrison M, et al. Dysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis. 2010;16:2034–42.PubMedCrossRef Kang S, Denman SE, Morrison M, et al. Dysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis. 2010;16:2034–42.PubMedCrossRef
118.
119.
go back to reference Pascal V, Pozuelo M, Borruel N, et al. A microbial signature for Crohn’s disease. Gut. 2017;66:813–22.PubMedCrossRef Pascal V, Pozuelo M, Borruel N, et al. A microbial signature for Crohn’s disease. Gut. 2017;66:813–22.PubMedCrossRef
120.
121.
go back to reference Franzosa EA, Sirota-Madi A, Avila-Pacheco J, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019;4:293–305.PubMedCrossRef Franzosa EA, Sirota-Madi A, Avila-Pacheco J, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019;4:293–305.PubMedCrossRef
122.
go back to reference Moustafa A, Li W, Anderson EL, et al. Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease. Clin Transl Gastroenterol. 2018;9:e132.PubMedPubMedCentralCrossRef Moustafa A, Li W, Anderson EL, et al. Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease. Clin Transl Gastroenterol. 2018;9:e132.PubMedPubMedCentralCrossRef
123.
go back to reference Papa E, Docktor M, Smillie C, et al. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS ONE. 2012;7:e39242.PubMedPubMedCentralCrossRef Papa E, Docktor M, Smillie C, et al. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS ONE. 2012;7:e39242.PubMedPubMedCentralCrossRef
124.
go back to reference Lewis JD, Chen EZ, Baldassano RN, et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe. 2015;18:489–500.PubMedPubMedCentralCrossRef Lewis JD, Chen EZ, Baldassano RN, et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe. 2015;18:489–500.PubMedPubMedCentralCrossRef
125.
go back to reference de Souza HSP, Fiocchi C, Iliopoulos D. The IBD interactome: an integrated view of aetiology, pathogenesis and therapy. Nat Rev Gastroenterol Hepatol. 2017;14:739–49.PubMedCrossRef de Souza HSP, Fiocchi C, Iliopoulos D. The IBD interactome: an integrated view of aetiology, pathogenesis and therapy. Nat Rev Gastroenterol Hepatol. 2017;14:739–49.PubMedCrossRef
126.
go back to reference Lloyd-Price J, Arze C, Ananthakrishnan AN, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569:655–62.PubMedPubMedCentralCrossRef Lloyd-Price J, Arze C, Ananthakrishnan AN, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569:655–62.PubMedPubMedCentralCrossRef
128.
130.
131.
go back to reference Wagner J, Maksimovic J, Farries G, et al. Bacteriophages in gut samples from pediatric Crohn’s disease patients: metagenomic analysis using 454 pyrosequencing. Inflamm Bowel Dis. 2013;19:1598–608.PubMedCrossRef Wagner J, Maksimovic J, Farries G, et al. Bacteriophages in gut samples from pediatric Crohn’s disease patients: metagenomic analysis using 454 pyrosequencing. Inflamm Bowel Dis. 2013;19:1598–608.PubMedCrossRef
132.
133.
go back to reference McCole DF. IBD candidate genes and intestinal barrier regulation. Inflamm Bowel Dis. 2014;20:1829–49.PubMedCrossRef McCole DF. IBD candidate genes and intestinal barrier regulation. Inflamm Bowel Dis. 2014;20:1829–49.PubMedCrossRef
134.
go back to reference Strober W, Fuss IJ, Blumberg RS. The immunology of mucosal models of inflammation. Annu Rev Immunol. 2002;20:495–549.PubMedCrossRef Strober W, Fuss IJ, Blumberg RS. The immunology of mucosal models of inflammation. Annu Rev Immunol. 2002;20:495–549.PubMedCrossRef
135.
go back to reference Ruffolo C, Scarpa M, Faggian D, et al. Subclinical intestinal inflammation in patients with Crohn’s disease following bowel resection: a smoldering fire. J Gastrointest Surg. 2010;14:24–31.PubMedCrossRef Ruffolo C, Scarpa M, Faggian D, et al. Subclinical intestinal inflammation in patients with Crohn’s disease following bowel resection: a smoldering fire. J Gastrointest Surg. 2010;14:24–31.PubMedCrossRef
136.
go back to reference Gassler N, Rohr C, Schneider A, et al. Inflammatory bowel disease is associated with changes of enterocytic junctions. Am J Physiol Gastrointest Liver Physiol. 2001;281:G216–28.PubMedCrossRef Gassler N, Rohr C, Schneider A, et al. Inflammatory bowel disease is associated with changes of enterocytic junctions. Am J Physiol Gastrointest Liver Physiol. 2001;281:G216–28.PubMedCrossRef
137.
go back to reference Zeissig S, Burgel N, Gunzel D, et al. Changes in expression and distribution of claudin 2, 5 and 8 lead to discontinuous tight junctions and barrier dysfunction in active Crohn’s disease. Gut. 2007;56:61–72.PubMedCrossRef Zeissig S, Burgel N, Gunzel D, et al. Changes in expression and distribution of claudin 2, 5 and 8 lead to discontinuous tight junctions and barrier dysfunction in active Crohn’s disease. Gut. 2007;56:61–72.PubMedCrossRef
138.
go back to reference Di Narzo AF, Brodmerkel C, Telesco SE, et al. High-throughput identification of the plasma proteomic signature of inflammatory bowel disease. J Crohns Colitis. 2019;13:462–71.PubMedCrossRef Di Narzo AF, Brodmerkel C, Telesco SE, et al. High-throughput identification of the plasma proteomic signature of inflammatory bowel disease. J Crohns Colitis. 2019;13:462–71.PubMedCrossRef
139.
go back to reference Katakura K, Lee J, Rachmilewitz D, et al. Toll-like receptor 9-induced type I IFN protects mice from experimental colitis. J Clin Investig. 2005;115:695–702.PubMedCrossRefPubMedCentral Katakura K, Lee J, Rachmilewitz D, et al. Toll-like receptor 9-induced type I IFN protects mice from experimental colitis. J Clin Investig. 2005;115:695–702.PubMedCrossRefPubMedCentral
140.
141.
go back to reference Neurath MF, Finotto S, Glimcher LH. The role of Th1/Th2 polarization in mucosal immunity. Nat Med. 2002;8:567–73.PubMedCrossRef Neurath MF, Finotto S, Glimcher LH. The role of Th1/Th2 polarization in mucosal immunity. Nat Med. 2002;8:567–73.PubMedCrossRef
142.
go back to reference Vermeire S, Schreiber S, Petryka R, et al. Clinical remission in patients with moderate-to-severe Crohn’s disease treated with filgotinib (the FITZROY study): results from a phase 2, double-blind, randomised, placebo-controlled trial. Lancet. 2017;389:266–75.PubMedCrossRef Vermeire S, Schreiber S, Petryka R, et al. Clinical remission in patients with moderate-to-severe Crohn’s disease treated with filgotinib (the FITZROY study): results from a phase 2, double-blind, randomised, placebo-controlled trial. Lancet. 2017;389:266–75.PubMedCrossRef
143.
go back to reference Neurath MF. Current and emerging therapeutic targets for IBD. Nat Rev Gastroenterol Hepatol. 2017;14:269–78.PubMedCrossRef Neurath MF. Current and emerging therapeutic targets for IBD. Nat Rev Gastroenterol Hepatol. 2017;14:269–78.PubMedCrossRef
144.
go back to reference Lichtenstein GR. Comprehensive review: antitumor necrosis factor agents in inflammatory bowel disease and factors implicated in treatment response. Therap Adv Gastroenterol. 2013;6:269–93.PubMedPubMedCentralCrossRef Lichtenstein GR. Comprehensive review: antitumor necrosis factor agents in inflammatory bowel disease and factors implicated in treatment response. Therap Adv Gastroenterol. 2013;6:269–93.PubMedPubMedCentralCrossRef
145.
go back to reference Friedrich M, Pohin M, Powrie F. Cytokine networks in the pathophysiology of inflammatory bowel disease. Immunity. 2019;50:992–1006.PubMedCrossRef Friedrich M, Pohin M, Powrie F. Cytokine networks in the pathophysiology of inflammatory bowel disease. Immunity. 2019;50:992–1006.PubMedCrossRef
146.
go back to reference Lu K, Knutson CG, Wishnok JS, et al. Serum metabolomics in a Helicobacter hepaticus mouse model of inflammatory bowel disease reveal important changes in the microbiome, serum peptides, and intermediary metabolism. J Proteome Res. 2012;11:4916–26.PubMedPubMedCentralCrossRef Lu K, Knutson CG, Wishnok JS, et al. Serum metabolomics in a Helicobacter hepaticus mouse model of inflammatory bowel disease reveal important changes in the microbiome, serum peptides, and intermediary metabolism. J Proteome Res. 2012;11:4916–26.PubMedPubMedCentralCrossRef
148.
go back to reference Agouridis AP, Elisaf M, Milionis HJ. An overview of lipid abnormalities in patients with inflammatory bowel disease. Ann Gastroenterol. 2011;24:181–7.PubMedPubMedCentral Agouridis AP, Elisaf M, Milionis HJ. An overview of lipid abnormalities in patients with inflammatory bowel disease. Ann Gastroenterol. 2011;24:181–7.PubMedPubMedCentral
149.
go back to reference Fan F, Mundra PA, Fang L, et al. Lipidomic profiling in inflammatory bowel disease: comparison between ulcerative colitis and Crohn’s disease. Inflamm Bowel Dis. 2015;21:1511–8.PubMedCrossRef Fan F, Mundra PA, Fang L, et al. Lipidomic profiling in inflammatory bowel disease: comparison between ulcerative colitis and Crohn’s disease. Inflamm Bowel Dis. 2015;21:1511–8.PubMedCrossRef
150.
go back to reference Titz B, Gadaleta RM, Lo Sasso G, et al. Proteomics and lipidomics in inflammatory bowel disease research: from mechanistic insights to biomarker identification. Int J Mol Sci. 2018;19:2775.PubMedCentralCrossRef Titz B, Gadaleta RM, Lo Sasso G, et al. Proteomics and lipidomics in inflammatory bowel disease research: from mechanistic insights to biomarker identification. Int J Mol Sci. 2018;19:2775.PubMedCentralCrossRef
151.
go back to reference Scoville EA, Allaman MM, Brown CT, et al. Alterations in lipid, amino acid, and energy metabolism distinguish Crohn’s disease from ulcerative colitis and control subjects by serum metabolomic profiling. Metabolomics. 2018;14:17.PubMedCrossRef Scoville EA, Allaman MM, Brown CT, et al. Alterations in lipid, amino acid, and energy metabolism distinguish Crohn’s disease from ulcerative colitis and control subjects by serum metabolomic profiling. Metabolomics. 2018;14:17.PubMedCrossRef
152.
go back to reference Murgia A, Hinz C, Liggi S, et al. Italian cohort of patients affected by inflammatory bowel disease is characterised by variation in glycerophospholipid, free fatty acids and amino acid levels. Metabolomics. 2018;14:140.PubMedCrossRef Murgia A, Hinz C, Liggi S, et al. Italian cohort of patients affected by inflammatory bowel disease is characterised by variation in glycerophospholipid, free fatty acids and amino acid levels. Metabolomics. 2018;14:140.PubMedCrossRef
153.
go back to reference Contijoch EJ, Britton GJ, Yang C, et al. Gut microbiota density influences host physiology and is shaped by host and microbial factors. Elife. 2019;8:e40553.PubMedPubMedCentralCrossRef Contijoch EJ, Britton GJ, Yang C, et al. Gut microbiota density influences host physiology and is shaped by host and microbial factors. Elife. 2019;8:e40553.PubMedPubMedCentralCrossRef
156.
go back to reference Waldschmitt N, Metwaly A, Fischer S, et al. Microbial signatures as a predictive tool in IBD-pearls and pitfalls. Inflamm Bowel Dis. 2018;24:1123–32.PubMedCrossRef Waldschmitt N, Metwaly A, Fischer S, et al. Microbial signatures as a predictive tool in IBD-pearls and pitfalls. Inflamm Bowel Dis. 2018;24:1123–32.PubMedCrossRef
157.
go back to reference Bercovici S, Meek C, Wexler Y, et al. Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping. Bioinformatics. 2010;26:i175–82.PubMedPubMedCentralCrossRef Bercovici S, Meek C, Wexler Y, et al. Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping. Bioinformatics. 2010;26:i175–82.PubMedPubMedCentralCrossRef
158.
go back to reference Fang K, Grisham MB, Kevil CG. Application of comparative transcriptional genomics to identify molecular targets for pediatric IBD. Front Immunol. 2015;6:165.PubMedPubMedCentralCrossRef Fang K, Grisham MB, Kevil CG. Application of comparative transcriptional genomics to identify molecular targets for pediatric IBD. Front Immunol. 2015;6:165.PubMedPubMedCentralCrossRef
Metadata
Title
Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine
Authors
Manoj Kumar
Mathieu Garand
Souhaila Al Khodor
Publication date
01-12-2019
Publisher
BioMed Central
Published in
Journal of Translational Medicine / Issue 1/2019
Electronic ISSN: 1479-5876
DOI
https://doi.org/10.1186/s12967-019-02174-1

Other articles of this Issue 1/2019

Journal of Translational Medicine 1/2019 Go to the issue