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

Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes

(2017) Joana C. Xavier et al.   METABOLIC ENGINEERING

Prediction of metabolic fluxes from gene expression data with Huber penalty convex optimization function

(2017) Shao-Wu Zhang et al.   Molecular BioSystems

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

(2017) Eugen Bauer et al.   PLoS Computational Biology

Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease

(2016) Robert Häsler et al.   GUT

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice

(2016) Hubert Plovier et al.   NATURE MEDICINE

Oscillospira : a Central, Enigmatic Component of the Human Gut Microbiota

(2016) Tom Konikoff et al.   TRENDS IN MICROBIOLOGY

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

Using Genome-scale Models to Predict Biological Capabilities

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

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes

(2015) Sebastian Kolinko et al.   ENVIRONMENTAL MICROBIOLOGY

Identification of an anti-inflammatory protein fromFaecalibacterium prausnitzii, a commensal bacterium deficient in Crohn’s disease

(2015) E Quévrain et al.   GUT

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal

(2015) Thi Phuong Nam Bui et al.   Nature Communications

Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating

(2015) Páraic Ó Cuív et al.   Scientific Reports

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

(2015) Zachary A. King et al.   PLoS Computational Biology

Species interactions differ in their genetic robustness

(2015) Lon M. Chubiz et al.   Frontiers in Microbiology

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

(2015) Eugen Bauer et al.   Microbiome

Fecal Microbiota Transplant for Treatment of Clostridium difficile Infection in Immunocompromised Patients

(2014) Colleen R Kelly et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods

(2014) Petr Baldrian et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Nutritional requirements and media development for Lactococcus lactis IL1403

(2014) Kadri Aller et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

(2014) Daniel S Weaver et al.   BMC Systems Biology

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

(2014) Ibrahim E El-Semman et al.   BMC Systems Biology

Refining metabolic models and accounting for regulatory effects

(2014) Joonhoon Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Effect of diet on the intestinal microbiota and its activity

(2014) Erwin G. Zoetendal et al.   CURRENT OPINION IN GASTROENTEROLOGY

Bile acids and the gut microbiome

(2014) Jason M. Ridlon et al.   CURRENT OPINION IN GASTROENTEROLOGY

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

(2014) Jennifer D Rocca et al.   ISME Journal

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

(2014) A. Heinken et al.   JOURNAL OF BACTERIOLOGY

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

(2014) J. Carrera et al.   Molecular Systems Biology

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

(2014) Raphy Zarecki et al.   PLoS Computational Biology

Methods for integration of transcriptomic data in genome-scale metabolic models

(2014) Min Kyung Kim et al.   Computational and Structural Biotechnology Journal

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

(2013) Pavel S Novichkov et al.   BMC GENOMICS

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models

(2013) J. P. Faria et al.   BRIEFINGS IN BIOINFORMATICS

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Comparative Metabolic Systems Analysis of Pathogenic Burkholderia

(2013) J. A. Bartell et al.   JOURNAL OF BACTERIOLOGY

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks

(2013) Sriram Chandrasekaran et al.   PLoS Computational Biology

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

(2013) Benjamin Steeb et al.   PLoS Pathogens

Molecular Analysis of Model Gut Microbiotas by Imaging Mass Spectrometry and Nanodesorption Electrospray Ionization Reveals Dietary Metabolite Transformations

(2012) Christopher M. Rath et al.   ANALYTICAL CHEMISTRY

Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies

(2012) Bettina M Länger et al.   BMC Systems Biology

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

(2012) Xueyang Feng et al.   BMC Systems Biology

Computational systems biology and in silico modeling of the human microbiome

(2012) E. Borenstein   BRIEFINGS IN BIOINFORMATICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Towards metagenome-scale models for industrial applications—the case of Lactic Acid Bacteria

(2012) Filipe Branco dos Santos et al.   CURRENT OPINION IN BIOTECHNOLOGY

Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota

(2012) Michael Graham Espey   FREE RADICAL BIOLOGY AND MEDICINE

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

(2012) Anthony A. Fodor et al.   PLoS One

Constraint-based modeling analysis of the metabolism of two Pelobacter species

(2011) Jun Sun et al.   BMC Systems Biology

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

(2011) Eleftheria Tzamali et al.   BMC Systems Biology

Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

(2011) Delphine M. Saulnier et al.   PLoS One

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing

(2010) Fahimeh Salimi et al.   Biotechnology Journal

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1

(2010) Martin I Sigurdsson et al.   BMC Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Genome-scale analyses of health-promoting bacteria: probiogenomics

(2008) Marco Ventura et al.   NATURE REVIEWS MICROBIOLOGY