Successful Dietary Therapy in Paediatric Crohn’s Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls

Gut Microbiota Reshaped by Pectin Treatment Improves Liver Steatosis in Obese Mice

(2021) Camille Houron et al.   Nutrients

Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolome

(2021) Benoit Chassaing et al.   GASTROENTEROLOGY

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

(2020) Sidhartha R. Sinha et al.   Cell Host & Microbe

Metabonomics and the gut microbiome associated with primary response to anti-TNF therapy in Crohn’s disease

(2020) N S Ding et al.   Journal of Crohns & Colitis

Diet should be a tool for researchers, not a treatment

(2020) Peter J. Turnbaugh   NATURE

Dietary Therapies Induce Rapid Response and Remission in Pediatric Patients With Active Crohn’s Disease

(2020) Rotem Sigall Boneh et al.   Clinical Gastroenterology and Hepatology

Past and Future Burden of Inflammatory Bowel Diseases Based on Modeling of Population-based Data

(2019) Stephanie Coward et al.   GASTROENTEROLOGY

Microbiota fermentation-NLRP3 axis shapes the impact of dietary fibres on intestinal inflammation

(2019) Vishal Singh et al.   GUT

Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids

(2019) Nijiati Abulizi et al.   Nutrients

Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases

(2019) Serena Sanna et al.   NATURE GENETICS

DOP42 Dietary therapies induce rapid response and remission in active paediatric Crohn’s disease

(2019) R Sigall Boneh et al.   Journal of Crohns & Colitis

Emerging roles of bile acids in mucosal immunity and inflammation

(2019) Mei Lan Chen et al.   Mucosal Immunology

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

The reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction

(2019) Michael Logan et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients with Inflammatory Bowel Diseases

(2019) Konrad Aden et al.   GASTROENTEROLOGY

Understanding the multifaceted roles of the phosphoenolpyruvate: Phosphotransferase system in regulation of Salmonella virulence using a mutant defective in ptsI and crr expression

(2019) Sangyoung Lim et al.   MICROBIOLOGICAL RESEARCH

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses

(2019) Sara Vieira-Silva et al.   Nature Microbiology

Predictors of anti-TNF treatment failure in anti-TNF-naive patients with active luminal Crohn's disease: a prospective, multicentre, cohort study

(2019) Nicholas A Kennedy et al.   Lancet Gastroenterology & Hepatology

Crohn’s Disease Exclusion Diet Plus Partial Enteral Nutrition Induces Sustained Remission in a Randomized Controlled Trial

(2019) Arie Levine et al.   GASTROENTEROLOGY

The relationship between fecal bile acids and microbiome community structure in pediatric Crohn’s disease

(2019) Jessica Connors et al.   ISME Journal

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki et al.   Cell Host & Microbe

Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice

(2018) Sean R. Llewellyn et al.   GASTROENTEROLOGY

Evolving role of diet in the pathogenesis and treatment of inflammatory bowel diseases

(2018) Arie Levine et al.   GUT

The Fructose-Specific Phosphotransferase System of Klebsiella pneumoniae is regulated by global regulator CRP and link to virulence and growth

(2018) Disi Lin et al.   INFECTION AND IMMUNITY

Phosphoenolpyruvate phosphotransferase system components positively regulate Klebsiella biofilm formation

(2018) Yu-Tze Horng et al.   JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION

Global Variation in Use of Enteral Nutrition for Pediatric Crohn Disease

(2018) Morgan Lawley et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

(2018) Gavin M. Douglas et al.   Microbiome

Treatment of Active Crohn’s Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition

(2018) V. Svolos et al.   GASTROENTEROLOGY

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Exclusive Enteral Nutrition Therapy in Paediatric Crohn’s Disease Results in Long-term Avoidance of Corticosteroids: Results of a Propensity-score Matched Cohort Analysis

(2017) Jessica Connors et al.   Journal of Crohns & Colitis

Differences in Outcomes Over Time With Exclusive Enteral Nutrition Compared With Steroids in Children With Mild to Moderate Crohn’s Disease: Results From the GROWTH CD Study

(2017) Noa Cohen-Dolev et al.   Journal of Crohns & Colitis

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred

(2017) Umer Zeeshan Ijaz et al.   PLoS One

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

(2016) Annika Wahlström et al.   Cell Metabolism

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition

(2015) Christopher Quince et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Two-Year Outcomes After Exclusive Enteral Nutrition Induction Are Superior to Corticosteroids in Pediatric Crohn’s Disease Treated Early with Thiopurines

(2015) Zubin Grover et al.   DIGESTIVE DISEASES AND SCIENCES

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohnʼs Disease

(2015) Dale Lee et al.   INFLAMMATORY BOWEL DISEASES

Toward Enteral Nutrition in the Treatment of Pediatric Crohn Disease in Canada: A Workshop to Identify Barriers and Enablers

(2015) Johan Van Limbergen et al.   Canadian Journal of Gastroenterology and Hepatology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Comparison of Outcomes Parameters for Induction of Remission in New Onset Pediatric Crohnʼs Disease

(2014) Arie Levine et al.   INFLAMMATORY BOWEL DISEASES

Consensus guidelines of ECCO/ESPGHAN on the medical management of pediatric Crohn's disease

(2014) F.M. Ruemmele et al.   Journal of Crohns & Colitis

The Bacterial Phosphoenolpyruvate:Carbohydrate Phosphotransferase System: Regulation by Protein Phosphorylation and Phosphorylation-Dependent Protein-Protein Interactions

(2014) Josef Deutscher et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities

(2014) Mahdi Shafiei et al.   PLoS Computational Biology

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases

(2012) Henri Duboc et al.   GUT

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mathematical weighting of the pediatric Crohnʼs disease activity index (PCDAI) and comparison with its other short versions

(2011) Dan Turner et al.   INFLAMMATORY BOWEL DISEASES

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Effect of apple intake on fecal microbiota and metabolites in humans

(2010) Kenji Shinohara et al.   ANAEROBE

Diet, gut microbiota and immune responses

(2010) Kendle M Maslowski et al.   NATURE IMMUNOLOGY