Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

Gut microbiota-derived metabolites as key actors in inflammatory bowel disease

(2020) Aonghus Lavelle et al.   Nature Reviews Gastroenterology & Hepatology

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome

(2020) Ines Thiele et al.   Molecular Systems Biology

Microbial butyrate synthesis indicates therapeutic efficacy of azathioprine in IBD patients

(2020) M Effenberger et al.   Journal of Crohns & Colitis

Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism

(2020) Amira Metwaly et al.   Nature Communications

Microbial network disturbances in relapsing refractory Crohn’s disease

(2019) Bahtiyar Yilmaz et al.   NATURE MEDICINE

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

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

(2019) Jason Lloyd-Price et al.   NATURE

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

(2019) Almut Heinken et al.   Microbiome

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

Hydrogen Sulfide as a Toxic Product in the Small–Large Intestine Axis and its Role in IBD Development

(2019) Ivan Kushkevych et al.   Journal of Clinical Medicine

Hydrogen sulfide: an agent of stability at the microbiome-mucosa interface

(2018) John L. Wallace et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data

(2018) Jasmine Chong et al.   BIOINFORMATICS

Gut Microbiota Regulation of Tryptophan Metabolism in Health and Disease

(2018) Allison Agus et al.   Cell Host & Microbe

Gut Microbiota as a Therapeutic Target for Metabolic Disorders

(2018) Hirofumi Okubo et al.   CURRENT MEDICINAL CHEMISTRY

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe

(2018) Santosh Lamichhane et al.   METHODS

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

(2018) Federico Baldini et al.   BIOINFORMATICS

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

A microbial signature for Crohn's disease

(2017) Victoria Pascal et al.   GUT

P478 The current place of probiotics in treatment of pouchitis: systematic review

(2017) L. Lichtenstein et al.   Journal of Crohns & Colitis

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy

(2017) Heitor S. P. de Souza et al.   Nature Reviews Gastroenterology & Hepatology

A role for bacterial urease in gut dysbiosis and Crohn’s disease

(2017) Josephine Ni et al.   Science Translational Medicine

Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients

(2017) Maria Laura Santoru et al.   Scientific Reports

Treatment with chondroitin sulfate to modulate inflammation and atherogenesis in obesity

(2016) Pedro Melgar-Lesmes et al.   ATHEROSCLEROSIS

Diet–microbiota interactions as moderators of human metabolism

(2016) Justin L. Sonnenburg et al.   NATURE

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sulfide as a Mucus Barrier-Breaker in Inflammatory Bowel Disease?

(2016) Noortje Ijssennagger et al.   TRENDS IN MOLECULAR MEDICINE

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

(2016) Maike K. Aurich et al.   Frontiers in Physiology

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

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

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

Effect of Chondroitin Sulphate on Pro-Inflammatory Mediators and Disease Activity in Patients with Inflammatory Bowel Disease

(2015) P.M. Linares et al.   DIGESTION

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

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

A decrease of the butyrate-producing speciesRoseburia hominisandFaecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis

(2013) Kathleen Machiels et al.   GUT

Serum Metabolic Profiling in Inflammatory Bowel Disease

(2012) Horace R. T. Williams et al.   DIGESTIVE DISEASES AND SCIENCES

The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic–anoxic interphases

(2012) M Tanweer Khan et al.   ISME Journal

Urinary NMR metabolomic profiles discriminate inflammatory bowel disease from healthy

(2012) Natasha S. Stephens et al.   Journal of Crohns & Colitis

Quantitative Metabolomic Profiling of Serum, Plasma, and Urine by 1H NMR Spectroscopy Discriminates between Patients with Inflammatory Bowel Disease and Healthy Individuals

(2012) Rudolf Schicho et al.   JOURNAL OF PROTEOME RESEARCH

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH