Reference health
The gut microbiota and inflammatory bowel diseases
105/105 checkable references clean · checked 2026-07-23
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
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The 105 checked references that resolve
resolves10.1136/gut.52.2.237
Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon
resolves10.1136/gut.2003.025403
Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease
resolves10.1136/gut.2005.073817
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach
resolves10.1128/JCM.01004-06
Differences between Tissue-Associated Intestinal Microfloras of Patients with Crohn's Disease and Ulcerative Colitis
resolves10.1073/pnas.0706625104
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
resolves10.1038/ng.3359
Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations
resolves10.1038/nature11582
Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease
resolves10.1038/ng.764
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47
resolves10.1038/ng.717
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
resolves10.1038/35079114
A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease
resolves10.1038/35079107
Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease
resolves10.1038/nature07416
A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells
resolves10.1053/j.gastro.2011.02.048
Autophagy, Microbial Sensing, Endoplasmic Reticulum Stress, and Epithelial Function in Inflammatory Bowel Disease
resolves10.1073/pnas.0907722106
Nod2 is required for the regulation of commensal microbiota in the intestine
resolves10.1002/ibd.21339
Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases
resolves10.1186/s13073-014-0107-1
Complex host genetics influence the microbiome in inflammatory bowel disease
resolves10.1136/gutjnl-2012-304214
The impact of Crohn's disease genes on healthy human gut microbiota: a pilot study
resolves10.1053/j.gastro.2014.07.023
The Diagnostic Approach to Monogenic Very Early Onset Inflammatory Bowel Disease
resolves10.1056/NEJMoa0907206
Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor
resolves10.1007/s11882-012-0286-z
Interleukin-10 and Interleukin-10–Receptor Defects in Inflammatory Bowel Disease
resolves10.1053/j.gastro.2012.04.045
Loss of Interleukin-10 Signaling and Infantile Inflammatory Bowel Disease: Implications for Diagnosis and Therapy
resolves10.1053/j.gastro.2014.06.005
Variants in Nicotinamide Adenine Dinucleotide Phosphate Oxidase Complex Components Determine Susceptibility to Very Early Onset Inflammatory Bowel Disease
resolves10.1053/j.gastro.2014.01.015
Mutations in Tetratricopeptide Repeat Domain 7A Result in a Severe Form of Very Early Onset Inflammatory Bowel Disease
resolves10.1080/003655200451207
Concordance of Inflammatory Bowel Disease among Danish Twins: Results of a Nationwide Study
resolves10.1016/S0016-5085(03)00385-8
Inflammatory bowel disease in a Swedish twin cohort: a long-term follow-up of concordance and clinical characteristics
resolves10.1002/ibd.20380
Epidemiology of inflammatory bowel disease in a German twin cohort: Results of a nationwide study
resolves10.1053/j.gastro.2007.03.034
A Nonsynonymous SNP in ATG16L1 Predisposes to Ileal Crohn’s Disease and Is Independent of CARD15 and IBD5
resolves10.1016/j.cell.2010.05.009
Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine
resolves10.1053/j.gastro.2011.10.001
Increasing Incidence and Prevalence of the Inflammatory Bowel Diseases With Time, Based on Systematic Review
resolves10.1093/aje/kwr400
Association of Repeated Exposure to Antibiotics With the Development of Pediatric Crohn's Disease--A Nationwide, Register-based Finnish Case-Control Study
resolves10.1542/peds.2011-3886
Antibiotic Exposure and IBD Development Among Children: A Population-Based Cohort Study
resolves10.1038/ajg.2014.246
Antibiotics Associated With Increased Risk of New-Onset Crohn’s Disease But Not Ulcerative Colitis: A Meta-Analysis
resolves10.1038/ajg.2015.52
Inflammatory Bowel Disease in Immigrants to Canada And Their Children: A Population-Based Cohort Study
resolves10.1002/ibd.21805
Cesarean section and offspringʼs risk of inflammatory bowel disease: A national cohort study
resolves10.1038/nature11400
Antibiotics in early life alter the murine colonic microbiome and adiposity
resolves10.1016/j.cell.2014.05.052
Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences
resolves10.1038/nm.3542
The microbiota regulates neutrophil homeostasis and host resistance to Escherichia coli K1 sepsis in neonatal mice
resolves10.1016/j.cell.2012.10.052
Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome
resolves10.1073/pnas.1005963107
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
resolves10.1038/nature11225
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice
resolves10.1016/j.cell.2012.04.037
Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota
resolves10.1126/science.aad2571
The maternal microbiota drives early postnatal innate immune development
resolves10.1073/pnas.0804812105
<i>Faecalibacterium prausnitzii</i>
is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
resolves10.1136/gutjnl-2013-304833
A decrease of the butyrate-producing species
<i>Roseburia hominis</i>
and
<i>Faecalibacterium prausnitzii</i>
defines dysbiosis in patients with ulcerative colitis
resolves10.1016/j.chom.2008.05.001
Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases
resolves10.1128/AEM.02810-10
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis
resolves10.1111/2041-210X.12114
Oligotyping: differentiating between closely related microbial taxa using 16S <scp>rRNA</scp> gene data
resolves10.1038/ismej.2014.195
Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
resolves10.1038/ctg.2013.9
Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach
resolves10.1126/science.1221789
Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis
resolves10.1080/00365520801935434
Fungi and inflammatory bowel diseases: Alterations of composition and diversity
resolves10.1097/MCG.0000000000000035
Dysbiosis of Gut Fungal Microbiota is Associated With Mucosal Inflammation in Crohn’s Disease
resolves10.1097/MIB.0000000000000454
Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease
resolves10.1016/j.chom.2015.09.008
Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease
resolves10.1053/j.gastro.2006.02.009
Candida albicans Is an Immunogen for Anti–Saccharomyces cerevisiae Antibody Markers of Crohn’s Disease
resolves10.1186/1471-2180-8-79
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis
resolves10.1016/j.chom.2007.05.004
The Bacillus subtilis Quorum-Sensing Molecule CSF Contributes to Intestinal Homeostasis via OCTN2, a Host Cell Membrane Transporter
resolves10.1053/j.gastro.2004.09.001
Probiotics inhibit nuclear factor-κB and induce heat shock proteins in colonic epithelial cells through proteasome inhibition
resolves10.1172/JCI44031
Colon-specific delivery of a probiotic-derived soluble protein ameliorates intestinal inflammation in mice through an EGFR-dependent mechanism
resolves10.1186/2049-2618-1-8
A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity
resolves10.1038/nature08530
Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43
resolves10.1126/science.1198469
Induction of Colonic Regulatory T Cells by Indigenous
<i>Clostridium</i>
Species
resolves10.1038/nature12331
Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota
resolves10.1126/science.1241165
The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T
<sub>reg</sub>
Cell Homeostasis
resolves10.1002/em.20546
DNA damage and toxicogenomic analyses of hydrogen sulfide in human intestinal epithelial FHs 74 Int cells
resolves10.1023/A:1006838231432
Sulfides impair short chain fatty acid β-oxidation at acyl-CoA dehydrogenase level in colonocytes: Implications for ulcerative colitis
resolves10.1002/ibd.22949
Decreased mucosal sulfide detoxification is related to an impaired butyrate oxidation in ulcerative colitis
resolves10.1099/00222615-35-4-238
The assessment of faecal flora in patients with inflammatory bowel disease by a simplified bacteriological technique
resolves10.1016/j.cell.2007.08.017
Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System
resolves10.1016/j.chom.2010.08.004
Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis
resolves10.1126/science.1232467
Host-Derived Nitrate Boosts Growth of
<i>E. coli</i>
in the Inflamed Gut
resolves10.1016/j.cell.2014.08.006
Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease
resolves10.1126/scitranslmed.aaa4877
Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy
resolves10.1038/nature14139
Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation
resolves10.1053/j.gastro.2011.06.064
Chronic Intestinal Inflammation Induces Stress-Response Genes in Commensal Escherichia coli
resolves10.1128/IAI.06181-11
Microevolution in
<i>fimH</i>
Gene of Mucosa-Associated Escherichia coli Strains Isolated from Pediatric Patients with Inflammatory Bowel Disease
resolves10.1371/journal.ppat.1003141
Point Mutations in FimH Adhesin of Crohn's Disease-Associated Adherent-Invasive Escherichia coli Enhance Intestinal Inflammatory Response
resolves10.1186/gb-2012-13-9-r79
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
resolves10.1073/pnas.1116053109
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
resolves10.1097/01.MIB.0000437495.30052.be
Effect of Probiotics on Inducing Remission and Maintaining Therapy in Ulcerative Colitis, Crohnʼs Disease, and Pouchitis
resolves10.1016/j.cgh.2013.02.021
Saccharomyces boulardii Does Not Prevent Relapse of Crohn's Disease
resolves10.3748/wjg.v21.i17.5359
Fecal microbiota transplantation as novel therapy in gastroenterology: A systematic review
resolves10.1038/ajg.2013.257
Temporal Bacterial Community Dynamics Vary Among Ulcerative Colitis Patients After Fecal Microbiota Transplantation
resolves10.1053/j.gastro.2015.03.045
Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis
resolves10.1128/mBio.00322-16
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation
The 1 reference without a DOI — listed, not checked
no DOI — not checkedMetagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria
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