Understanding the host-microbe interactions using metabolic modeling

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

(2020) Christian Diener et al.   mSystems

Macroecological dynamics of gut microbiota

(2020) Brian W. Ji et al.   Nature Microbiology

Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics

(2020) Ellen Kuang et al.   Metabolites

Occurrence of the potent mutagens 2- nitrobenzanthrone and 3-nitrobenzanthrone in fine airborne particles

(2019) Aldenor G. Santos et al.   Scientific Reports

Fecal microbiota transplantation for treatment of recurrent C. difficile infection: An updated randomized controlled trial meta-analysis

(2019) Wenjia Hui et al.   PLoS One

Structural variation in the gut microbiome associates with host health

(2019) David Zeevi 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

Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling

(2019) Chan et al.   Processes

Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy

(2019) Rosina Pryor et al.   CELL

A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators

(2019) Loïc Martinet et al.   mBio

Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

(2019) Johannes Hertel et al.   Cell Reports

Treatment with gut bifidobacteria improves hippocampal plasticity and cognitive behavior in adult healthy rats

(2019) G. Talani et al.   NEUROPHARMACOLOGY

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

(2019) N. T. Devika et al.   Scientific Reports

Dysbiosis of gut microbiota and microbial metabolites in Parkinson’s Disease

(2018) Meng-Fei Sun et al.   AGEING RESEARCH REVIEWS

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

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Structural basis for recognition of diverse antidepressants by the human serotonin transporter

(2018) Jonathan A. Coleman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis

(2018) Promi Das et al.   PLoS One

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

(2018) Liping Zhao et al.   SCIENCE

Structural basis for recognition of diverse antidepressants by the human serotonin transporter

(2018) Jonathan A. Coleman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Probiotic Species in the Modulation of Gut Microbiota: An Overview

(2018) Md. Abul Kalam Azad et al.   Biomed Research International

Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

(2018) Alberto Robador et al.   Frontiers in Microbiology

Towards predicting the environmental metabolome from metagenomics with a mechanistic model

(2018) Daniel R. Garza et al.   Nature Microbiology

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

(2018) Eugen Bauer et al.   mSystems

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Challenges in modeling the human gut microbiome

(2018) Parizad Babaei et al.   NATURE BIOTECHNOLOGY

Reply to "Challenges in modeling the human gut microbiome"

(2018) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington's disease

(2018) Geraldine Kong et al.   NEUROBIOLOGY OF DISEASE

Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection

(2018) T. J. De Wolfe et al.   PLoS One

Systems analysis of intracellular pH vulnerabilities for cancer therapy

(2018) Erez Persi et al.   Nature Communications

A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

(2018) Osvaldo D. Kim et al.   Frontiers in Microbiology

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

(2018) Gregory L. Medlock et al.   Cell Systems

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

(2018) Federico Baldini et al.   BIOINFORMATICS

Contradictory Results in Microbiome Science Exemplified by Recent Drosophila Research

(2018) Angela E. Douglas   mBio

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants

(2018) Katri Korpela et al.   Microbiome

Biomedical applications of cell- and tissue-specific metabolic network models

(2017) Hamideh Fouladiha et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

(2017) J. R. Bedarf et al.   Genome 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

Gut microbiome alterations in Alzheimer’s disease

(2017) Nicholas M. Vogt et al.   Scientific Reports

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

(2016) Timothy R. Sampson et al.   CELL

Constraint-based stoichiometric modelling from single organisms to microbial communities

(2016) Willi Gottstein et al.   Journal of the Royal Society Interface

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

(2016) Pranjul Shah et al.   Nature Communications

Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers

(2016) A P Allen et al.   Translational Psychiatry

Starch and starch hydrolysates are favorable carbon sources for Bifidobacteria in the human gut

(2015) Songling Liu et al.   BMC MICROBIOLOGY

A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood

(2015) Laura Steenbergen et al.   BRAIN BEHAVIOR AND IMMUNITY

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

(2014) Jose A Gomez et al.   BMC BIOINFORMATICS

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

Dynamic flux balance analysis for synthetic microbial communities

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

Fecal microbiota transplantation as therapy for inflammatory bowel disease: A systematic review and meta-analysis

(2014) Ruben J. Colman et al.   Journal of Crohns & Colitis

The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

(2014) Colin Hill et al.   Nature Reviews Gastroenterology & Hepatology

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

(2014) Ali R. Zomorrodi et al.   ACS Synthetic Biology

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

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

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

A reliable simulator for dynamic flux balance analysis

(2012) K. Höffner et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

(2012) Henri Duboc et al.   GUT

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

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

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

Modeling the Fluid Dynamics in a Human Stomach to Gain Insight of Food Digestion

(2010) M.J. Ferrua et al.   JOURNAL OF FOOD SCIENCE

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

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Micromolar concentration of kynurenic acid in rat small intestine

(2008) D. Kuc et al.   AMINO ACIDS

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