Characterization of the gastrointestinal microbiota in health and inflammatory bowel disease. (Q37878446)

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1 February 2020

review article

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title

Characterization of the gastrointestinal microbiota in health and inflammatory bowel disease (English)

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inflammatory bowel diseases

1 February 2020

main subject

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1 February 2020

Mark Morrison

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Carl Kirkwood

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1 February 2020

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Michael A Kamm

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1 February 2020

author name string

Peter De Cruz

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1 February 2020

Lani Prideaux

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1 February 2020

Josef Wagner

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1 February 2020

Chris McSweeney

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publication date

20 May 2011

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Inflammatory Bowel Diseases

1 February 2020

published in

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volume

18

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issue

2

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1 February 2020

page(s)

372-390

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Ecological and evolutionary forces shaping microbial diversity in the human intestine

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Molecular monitoring of succession of bacterial communities in human neonates

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Quantification of Bifidobacterium spp., Escherichia coli and Clostridium difficile in faecal samples of breast-fed and formula-fed infants by real-time PCR.

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The composition of the faecal microflora in breastfed and bottle fed infants from birth to eight weeks

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The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life

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Aberrant composition of gut microbiota of allergic infants: a target of bifidobacterial therapy at weaning?

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Bifidobacterium pseudocatenulatum is associated with atopic eczema: A nested case-control study investigating the fecal microbiota of infants

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Fecal microbiota in sensitized wheezy and non-sensitized non-wheezy children: a nested case-control study

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Role of intestinal flora in the development of allergy

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The increase in the prevalence of asthma and allergy: food for thought

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Neonatal exposure with LPS and/or allergen prevents experimental allergic airways disease: development of tolerance using environmental antigens

21 January 2018

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Diversity of the human intestinal microbial flora

21 January 2018

1 reference

Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians

21 January 2018

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Assessing gut microbial diversity from feces and rectal mucosa

21 January 2018

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Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers

21 January 2018

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Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria

21 January 2018

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High temporal and inter-individual variation detected in the human ileal microbiota

21 January 2018

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A core gut microbiome in obese and lean twins

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Towards the human intestinal microbiota phylogenetic core

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Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

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Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach

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Symbiotic gut microbes modulate human metabolic phenotypes

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Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach

21 January 2018

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Host-bacterial mutualism in the human intestine

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Obesity alters gut microbial ecology

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The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice

21 January 2018

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Investigations into the influence of host genetics on the predominant eubacteria in the faecal microflora of children.

21 January 2018

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A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes

21 January 2018

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Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection

21 January 2018

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Durable alteration of the colonic microbiota by the administration of donor fecal flora

21 January 2018

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Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases

21 January 2018

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Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface

21 January 2018

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Homeostasis and inflammation in the intestine

21 January 2018

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Endoplasmic reticulum stress in the intestinal epithelium and inflammatory bowel disease

21 January 2018

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Paneth cells and inflammation dance together in Crohn's disease

21 January 2018

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XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease

21 January 2018

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Endoplasmic reticulum stress: implications for inflammatory bowel disease pathogenesis

21 January 2018

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A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

21 January 2018

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Modulation of the intestinal microbiota alters colitis-associated colorectal cancer susceptibility

21 January 2018

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Nod2 is required for the regulation of commensal microbiota in the intestine

21 January 2018

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The genetics and immunopathogenesis of inflammatory bowel disease

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21 January 2018

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A microbial symbiosis factor prevents intestinal inflammatory disease

21 January 2018

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Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

21 January 2018

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Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine

21 January 2018

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Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity

21 January 2018

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An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system

21 January 2018

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Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

21 January 2018

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Molecular comparison of dominant microbiota associated with injured versus healthy mucosa in ulcerative colitis.

21 January 2018

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Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease

21 January 2018

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Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn's disease.

21 January 2018

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Enhanced Escherichia coli adherence and invasion in Crohn's disease and colon cancer

21 January 2018

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Mucosal flora in inflammatory bowel disease

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Mucosal and invading bacteria in patients with inflammatory bowel disease compared with controls.

21 January 2018

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Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease.

21 January 2018

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Ribosomal DNA sequence analysis of mucosa-associated bacteria in Crohn's disease

21 January 2018

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Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus.

21 January 2018

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Characterization of antibody responses against rectal mucosa-associated bacterial flora in patients with ulcerative colitis

21 January 2018

1 reference

Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease

21 January 2018

1 reference

Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease

21 January 2018

1 reference

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

21 January 2018

1 reference

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

21 January 2018

1 reference

Unstable composition of the fecal microbiota in ulcerative colitis during clinical remission

21 January 2018

1 reference

Dynamics of the mucosa-associated flora in ulcerative colitis patients during remission and clinical relapse

21 January 2018

1 reference

Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota.

21 January 2018

1 reference

Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis

21 January 2018

1 reference

Microbiota in pediatric inflammatory bowel disease.

21 January 2018

1 reference

Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray

21 January 2018

1 reference

Highlighting new phylogenetic specificities of Crohn's disease microbiota.

21 January 2018

1 reference

Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces

21 January 2018

1 reference

Virulence properties of Escherichia coli strains isolated from patients with inflammatory bowel disease

21 January 2018

1 reference

High prevalence of Escherichia coli belonging to the B2 D phylogenetic group in inflammatory bowel disease

21 January 2018

1 reference

Molecular characterization of rectal mucosa-associated bacterial flora in inflammatory bowel disease.

21 January 2018

1 reference

High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease

21 January 2018

1 reference

Quantitative analysis of bacterial DNA from Mycobacteria spp., Bacteroides vulgatus, and Escherichia coli in tissue samples from patients with inflammatory bowel diseases.

21 January 2018

1 reference

Molecular inventory of faecal microflora in patients with Crohn's disease

21 January 2018

1 reference

The assessment of faecal flora in patients with inflammatory bowel disease by a simplified bacteriological technique.

21 January 2018

1 reference

Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease

21 January 2018

1 reference

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives.

21 January 2018

1 reference

Mycobacterium avium subspecies paratuberculosis and Crohn's disease: a systematic review and meta-analysis

21 January 2018

1 reference

Detection of Mycobacterium avium subspecies paratuberculosis from patients with Crohn's disease using nucleic acid-based techniques: a systematic review and meta-analysis

21 January 2018

1 reference

On the action of methotrexate and 6-mercaptopurine on M. avium subspecies paratuberculosis

21 January 2018

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On the action of 5-amino-salicylic acid and sulfapyridine on M. avium including subspecies paratuberculosis

21 January 2018

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Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn's disease

21 January 2018

1 reference

Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease

21 January 2018

1 reference

Adherent-invasive Escherichia coli in inflammatory bowel disease

21 January 2018

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Pathogenic Escherichia coli

21 January 2018

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Type 1 pili-mediated adherence of Escherichia coli strain LF82 isolated from Crohn's disease is involved in bacterial invasion of intestinal epithelial cells.

21 January 2018

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Regulatory and functional co-operation of flagella and type 1 pili in adhesive and invasive abilities of AIEC strain LF82 isolated from a patient with Crohn's disease.

21 January 2018

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The flagellar sigma factor FliA regulates adhesion and invasion of Crohn disease-associated Escherichia coli via a cyclic dimeric GMP-dependent pathway.

21 January 2018

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OmpC and the sigma(E) regulatory pathway are involved in adhesion and invasion of the Crohn's disease-associated Escherichia coli strain LF82.

21 January 2018

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Involvement of lipoprotein NlpI in the virulence of adherent invasive Escherichia coli strain LF82 isolated from a patient with Crohn's disease

21 January 2018

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The oxidoreductase DsbA plays a key role in the ability of the Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 to resist macrophage killing

21 January 2018

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Pathogenic agents in inflammatory bowel diseases

21 January 2018

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Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly

21 January 2018

1 reference

CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease

21 January 2018

1 reference

Adherent invasive Escherichia coli strains from patients with Crohn's disease survive and replicate within macrophages without inducing host cell death

21 January 2018

1 reference

CARD15 variants determine a disturbed early response of monocytes to adherent-invasive Escherichia coli strain LF82 in Crohn's disease

21 January 2018

1 reference

Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease

21 January 2018

1 reference

Identification of a novel bacterial sequence associated with Crohn's disease

21 January 2018

1 reference

The clinical Pseudomonas fluorescens MFN1032 strain exerts a cytotoxic effect on epithelial intestinal cells and induces Interleukin-8 via the AP-1 signaling pathway

21 January 2018

1 reference

Pathogenic Yersinia DNA is detected in bowel and mesenteric lymph nodes from patients with Crohn's disease

21 January 2018

1 reference

Listeria monocytogenes and inflammatory bowel disease: detection of Listeria species in intestinal mucosal biopsies by real-time PCR.

21 January 2018

1 reference

Detection of Listeria monocytogenes by polymerase chain reaction in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls

21 January 2018

1 reference

Novel Burkholderiales 23S rRNA genes identified in ileal biopsy samples from children: preliminary evidence that a subtype is associated with perianal Crohn's disease

21 January 2018

1 reference

A pathobiont of the microbiota balances host colonization and intestinal inflammation.

21 January 2018

1 reference

Detection of enterohepatic and gastric helicobacter species in fecal specimens of children with Crohn's disease

21 January 2018

1 reference

Isolation of Helicobacter pylori from the intestinal mucosa of patients with Crohn's disease

21 January 2018

1 reference

Association between entero-hepatic Helicobacter species and Crohn's disease: a prospective cross-sectional study.

21 January 2018

1 reference

Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine

21 January 2018

1 reference

A Microbe-Dependent Viral Key to Crohn's Box

21 January 2018

1 reference

Candida albicans colonization and ASCA in familial Crohn's disease

21 January 2018

1 reference

Fungi and inflammatory bowel diseases: Alterations of composition and diversity

21 January 2018

1 reference

Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples

21 January 2018

1 reference

The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients

21 January 2018

1 reference

Inhibition of HDAC9 increases T regulatory cell function and prevents colitis in mice.

21 January 2018

1 reference

Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism

21 January 2018

1 reference

Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis

21 January 2018

1 reference

Structural shifts of mucosa-associated lactobacilli and Clostridium leptum subgroup in patients with ulcerative colitis

21 January 2018

1 reference

Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA.

21 January 2018

1 reference

Patchy distribution of mucosal lesions in ileal Crohn's disease is not linked to differences in the dominant mucosa-associated bacteria: a study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis

21 January 2018

1 reference

Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease.

21 January 2018

1 reference

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

21 January 2018

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Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces

21 January 2018

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Microbial ecology: human gut microbes associated with obesity

21 January 2018

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Double-blind crossover trial of metronidazole versus placebo in chronic unremitting pouchitis

21 January 2018

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Prophylaxis of pouchitis onset with probiotic therapy: a double-blind, placebo-controlled trial

21 January 2018

1 reference

A characterization of anaerobic colonization and associated mucosal adaptations in the undiseased ileal pouch.

21 January 2018

1 reference

The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing

21 January 2018

1 reference

Dysbiosis in pouchitis: evidence of unique microfloral patterns in pouch inflammation

21 January 2018

1 reference

Metagenomics: DNA sequencing of environmental samples.

21 January 2018

1 reference

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

21 January 2018

1 reference

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

21 January 2018

1 reference

Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients

21 January 2018

1 reference

OMICS-driven biomarker discovery in nutrition and health

21 January 2018

1 reference

Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract

21 January 2018

1 reference

Shotgun metaproteomics of the human distal gut microbiota

21 January 2018

1 reference

The discovery and validation of colorectal cancer biomarkers

21 January 2018

1 reference

An overview of proteomic and metabolomic technologies and their application to pregnancy research

21 January 2018

1 reference

Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism

21 January 2018

1 reference

Metabonomics in ulcerative colitis: diagnostics, biomarker identification, and insight into the pathophysiology

21 January 2018

1 reference

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

21 January 2018

1 reference

A genome-wide association study identifies novel risk loci for type 2 diabetes

21 January 2018

1 reference

Human metabolic phenotype diversity and its association with diet and blood pressure.

21 January 2018

1 reference

Opening up the "Black Box": metabolic phenotyping and metabolome-wide association studies in epidemiology

21 January 2018

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21 January 2018

1 reference

A 1H NMR-based metabonomic study of urine and plasma samples obtained from healthy human subjects

21 January 2018

1 reference

NMR-based metabonomics analysis of mouse urine and fecal extracts following oral treatment with the broad-spectrum antibiotic enrofloxacin (Baytril).

21 January 2018

1 reference

Metabolomics reveals metabolic biomarkers of Crohn's disease

21 January 2018

1 reference

Effect of intestinal microflora on the urinary metabolic profile of rats: a (1)H-nuclear magnetic resonance spectroscopy study

21 January 2018

1 reference

NMR spectroscopic-based metabonomic studies of urinary metabolite variation in acclimatizing germ-free rats

21 January 2018

1 reference

Characterization of inflammatory bowel disease with urinary metabolic profiling.

21 January 2018

1 reference

Metabolism of the colonic mucosa in patients with inflammatory bowel diseases: an in vitro proton magnetic resonance spectroscopy study.

21 January 2018

1 reference

The use of 1H magnetic resonance spectroscopy in inflammatory bowel diseases: distinguishing ulcerative colitis from Crohn's disease

21 January 2018

1 reference

21 January 2018

1 reference

Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study

21 January 2018

1 reference

Colonic microbiota signatures across five northern European countries

21 January 2018

1 reference

Intestinal microflora of Estonian and Swedish infants

21 January 2018

1 reference

Gut microbiota of children living in rural south Thailand and urban Singapore

21 January 2018

1 reference

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

21 January 2018

1 reference

Interactions and competition within the microbial community of the human colon: links between diet and health.

21 January 2018

1 reference

Disorders of a modern lifestyle: reconciling the epidemiology of inflammatory bowel diseases.

21 January 2018

1 reference

An update on the epidemiology of inflammatory bowel disease in Asia

21 January 2018

1 reference

Obesity and the human microbiome

21 January 2018

1 reference

Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability

21 January 2018

1 reference

Short-chain fatty acids: ready for prime time?

21 January 2018

1 reference

Regulation of short-chain fatty acid production

21 January 2018

1 reference

Butyrate-induced transcriptional changes in human colonic mucosa

21 January 2018

1 reference

Understanding the effects of diet on bacterial metabolism in the large intestine

21 January 2018

1 reference

Phylogenetic relationships of butyrate-producing bacteria from the human gut.

21 January 2018

1 reference

Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces

21 January 2018

1 reference

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale

21 January 2018

1 reference

The specificity of the interaction with intestinal bacterial fermentation by prebiotics determines their physiological efficacy

21 January 2018

1 reference

Low counts of Faecalibacterium prausnitzii in colitis microbiota.

21 January 2018

1 reference

Effects of dietary fiber on inflammatory bowel disease.

21 January 2018

1 reference

Hydrogen sulfide induces direct radical-associated DNA damage.

21 January 2018

1 reference

Significance of systemic endotoxaemia in inflammatory bowel disease

21 January 2018

1 reference

Colonic sulfide in pathogenesis and treatment of ulcerative colitis

21 January 2018

1 reference

Environmental influences on the high mortality from colorectal cancer in African Americans

21 January 2018

1 reference

The African way of life and colon cancer risk

21 January 2018

1 reference

Nutrition and colonic health: the critical role of the microbiota

21 January 2018

1 reference

Products of the colonic microbiota mediate the effects of diet on colon cancer risk.

21 January 2018

1 reference

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

21 January 2018

1 reference

Dietary risk factors for inflammatory bowel disease: a multicenter case-control study in Japan.

21 January 2018

1 reference

Imbalances in dietary consumption of fatty acids, vegetables, and fruits are associated with risk for Crohn's disease in children.

21 January 2018

1 reference

Diet as a risk factor for the development of ulcerative colitis

21 January 2018

1 reference

Influence of dietary factors on the clinical course of ulcerative colitis: a prospective cohort study

21 January 2018

1 reference

Clinical epidemiology of inflammatory bowel disease: Incidence, prevalence, and environmental influences

21 January 2018

1 reference

Childhood factors in ulcerative colitis and Crohn's disease. An international cooperative study

21 January 2018

1 reference

Pre-illness dietary factors in inflammatory bowel disease

21 January 2018

1 reference

Environmental factors in inflammatory bowel disease: a co-twin control study of a Swedish-Danish twin population

21 January 2018

1 reference

Environmental risk factors in paediatric inflammatory bowel diseases: a population based case control study

21 January 2018

1 reference

Depletion of luminal iron alters the gut microbiota and prevents Crohn's disease-like ileitis.

21 January 2018

1 reference

The effects of iron fortification on the gut microbiota in African children: a randomized controlled trial in Cote d'Ivoire

21 January 2018

1 reference

Faecal microbiota in breast-fed infants after antibiotic therapy

21 January 2018

1 reference

Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease

21 January 2018

1 reference

Specificities of the fecal microbiota in inflammatory bowel disease

21 January 2018

1 reference

Susceptibility of Human Metabolic Phenotypes to Dietary Modulation

21 January 2018

1 reference

Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent?

21 January 2018

1 reference

Body fatness and bevacizumab-based therapy in metastatic colorectal cancer

21 January 2018

1 reference