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

The Dimension of Time in Host-Microbiome Interactions

(2019) Giulia T. Uhr et al.   mSystems

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

(2019) Laurent Heirendt et al.   Nature Protocols

Identification of a gene encoding a flavoprotein involved in bile acid metabolism by the human gut bacterium Clostridium scindens ATCC 35704

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Modeling metabolism of the human gut microbiome

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Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12α-Hydroxysteroid Dehydrogenases from Bile Acid 7α-Dehydroxylating Human Gut Bacteria

(2018) Heidi Doden et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling

(2018) Manish Kumar et al.   METABOLIC ENGINEERING

Reply to "Challenges in modeling the human gut microbiome"

(2018) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin

(2018) Lulu Sun et al.   NATURE MEDICINE

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers

(2018) Vanessa L. Hale et al.   Genome Medicine

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

SteadyCom: Predicting microbial abundances while ensuring community stability

(2017) Siu Hung Joshua Chan et al.   PLoS Computational Biology

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

(2017) Kees C. H. van der Ark et al.   Microbiome

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides

(2017) Dmitry A. Ravcheev et al.   Frontiers in Genetics

Interaction of gut microbiota with bile acid metabolism and its influence on disease states

(2016) Christopher Staley et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2016) Annika Wahlström et al.   Cell Metabolism

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

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

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

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

A biosynthetic pathway for a prominent class of microbiota-derived bile acids

(2015) A Sloan Devlin et al.   Nature Chemical Biology

Systems biology of host-microbe metabolomics

(2015) Almut Heinken et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Glycan cross-feeding activities between bifidobacteria under in vitro conditions

(2015) Francesca Turroni et al.   Frontiers in Microbiology

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

(2015) Stefanía Magnúsdóttir et al.   Frontiers in Genetics

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

(2014) Christoph A. Thaiss et al.   CELL

Dynamic flux balance analysis for synthetic microbial communities

(2014) Michael A. Henson et al.   IET Systems Biology

Bacterial Bile Metabolising Gene Abundance in Crohn's, Ulcerative Colitis and Type 2 Diabetes Metagenomes

(2014) Alain Labbé et al.   PLoS One

A systems biology approach to studying the role of microbes in human health

(2012) Ines Thiele et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2012) Henri Duboc et al.   GUT

A framework for human microbiome research

(2012)   NATURE

In search of sustainable chemical processes: cloning, recombinant expression, and functional characterization of the 7α- and 7β-hydroxysteroid dehydrogenases from Clostridium absonum

(2011) Erica Elisa Ferrandi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

(2011) S. G. Thorleifsson et al.   BIOINFORMATICS

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(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

(2010) Terry Disz et al.   BMC BIOINFORMATICS

Removal of cholesterol by lactobacilli via incorporation and conversion to coprostanol

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High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome

(2008) B. V. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiotic gut microbes modulate human metabolic phenotypes

(2008) M. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA