Modeling metabolism of the human gut microbiome

The Sequence Alignment/Map format and SAMtools

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Structure, function and diversity of the healthy human microbiome

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Diet rapidly and reproducibly alters the human gut microbiome

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Human gut microbiome viewed across age and geography

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A metagenome-wide association study of gut microbiota in type 2 diabetes

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Obesity alters gut microbial ecology

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The impact of the gut microbiota on human health: an integrative view

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Gut microbiota composition correlates with diet and health in the elderly

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Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

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Microbial degradation of complex carbohydrates in the gut

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Artificial sweeteners induce glucose intolerance by altering the gut microbiota

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

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KBase: The United States Department of Energy Systems Biology Knowledgebase

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Bacteria as vitamin suppliers to their host: A gut microbiota perspective

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Diet dominates host genotype in shaping the murine gut microbiota

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

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A community-driven global reconstruction of human metabolism

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Host lifestyle affects human microbiota on daily timescales

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Metabolic dependencies drive species co-occurrence in diverse microbial communities

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

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Applications of genome‐scale metabolic reconstructions

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

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

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Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

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Metabolomics enables precision medicine: “A White Paper, Community Perspective”

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Competitive and cooperative metabolic interactions in bacterial communities

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Metabolic modeling of a mutualistic microbial community

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

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Molecular analysis of the gut microbiota of identical twins with Crohn's disease

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Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

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Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

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

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

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Contribution of microbial amino acids to amino acid homeostasis of the host

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The gut microbiota modulates host amino acid and glutathione metabolism in mice

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Computationally efficient flux variability analysis

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Environments that Induce Synthetic Microbial Ecosystems

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Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

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Optimization based automated curation of metabolic reconstructions

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

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Systems approach to refining genome annotation

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Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

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Understanding the interactions between bacteria in the human gut through metabolic modeling

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Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

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

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SteadyCom: Predicting microbial abundances while ensuring community stability

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Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

Heinken, A., Sahoo, S., Fleming, R. M. T., & Thiele, I. (2013) · Gut Microbes · doi:10.4161/gmic.22370 · Cited by 219 · see citing works

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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Functional and phylogenetic assembly of microbial communities in the human microbiome

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

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

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Effects of Alternative Dietary Substrates on Competition between Human Colonic Bacteria in an Anaerobic Fermentor System

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Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome

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Metabolic network modeling of microbial communities

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Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes <i>In Silico</i>

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fast G ap F ill : efficient gap filling in metabolic networks

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Systems biology constraint-based reconstruction and analysis

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

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Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

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Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

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

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Systems biology of host–microbe metabolomics

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Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers

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Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0Preprint

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Increased decision thresholds enhance information gathering performance in juvenile Obsessive-Compulsive Disorder (OCD)

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Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli

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The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

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Calibration and analysis of genome-based models for microbial ecology

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Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

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A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems

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Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction

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Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

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Building the power house: recent advances in mitochondrial studies through proteomics and systems biology

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Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

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Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome

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DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia

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Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individualsPreprint

Heinken, A., Ravcheev, D. A., Baldini, F., Heirendt, L., Fleming, R. M. T., & Thiele, I. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/229138 · Cited by 28 · see citing works

Species interactions differ in their genetic robustness

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Conditions for duality between fluxes and concentrations in biochemical networks

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Metabolic network-guided binning of metagenomic sequence fragments

Biggs, M. B., & Papin, J. A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv671 · Cited by 10 · see citing works

From metagenomic data to personalized computational microbiotas: Predicting dietary supplements for Crohn's diseasePreprint

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The Microbiota-Gut-Brain Axis

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

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Gut reactions: Breaking down xenobiotic–microbiome interactions

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Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

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Reconstructing organisms in silico: genome-scale models and their emerging applications

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A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

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Metabolic Engineering: Methodologies and Applications

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A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016

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The role of the microbiome in ovarian cancer: mechanistic insights into oncobiosis and to bacterial metabolite signaling

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Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics

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

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Understanding the host-microbe interactions using metabolic modeling

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Plant Genetics as a Tool for Manipulating Crop Microbiomes: Opportunities and Challenges

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The gut microbiota promotes the pathogenesis of schizophrenia via multiple pathways

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A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations

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Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids

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In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids

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Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies

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Factors Affecting Gut Microbiome in Daily Diet

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Gut microbiome-metabolome interactions predict host condition

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The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

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Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance

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Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

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The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence

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Computational Modeling of the Human Microbiome

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CRISPR-Cas9: A method for establishing rat models of drug metabolism and pharmacokinetics

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Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome

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Gut Microbiota and Human Body Interactions; Its Impact on Health: A Review

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Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies

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Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells

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Neoagaro-Oligosaccharides Ameliorate Chronic Restraint Stress-Induced Depression by Increasing 5-HT and BDNF in the Brain and Remodeling the Gut Microbiota of Mice

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Gut microbiota and gut tissue metabolites involved in development and prevention of depression

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What the Gut Tells the Brain—Is There a Link between Microbiota and Huntington’s Disease?

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First and second generation probiotic therapeutics for Inflammatory Bowel Disease

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Key Technologies for Progressing Discovery of Microbiome-Based Medicines

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An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community

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Gardenia Jasminoides Ameliorates Antibiotic-Associated Aggravation of DNCB-Induced Atopic Dermatitis by Restoring the Intestinal Microbiome Profile

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Hyperbaric oxygen improves depression‐like behaviors in chronic stress model mice by remodeling gut microbiota and regulating host metabolism

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Modelling microbial communities using biochemical resource allocation analysis

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Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth

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Material Engineering in Gut Microbiome and Human Health

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A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota

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

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Expanding the drug discovery space with predicted metabolite–target interactions

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Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses

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A Computational Framework for Studying Gut-Brain Axis in Autism Spectrum Disorder

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The interaction among Kluyveromyces marxianus G-Y4, Lacticaseibacillus paracasei GL1, and Lactobacillus helveticus SNA12 and signaling molecule AI-2 participate in the formation of biofilm

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Emerging tools and best practices for studying gut microbial community metabolism

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Not by (Good) Microbes Alone: Towards Immunocommensal Therapies

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Biogas starter from genome-scale data for methanogenic bioprocessing of protein waste

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Syntrophic splitting of central carbon metabolism in host cells bearing functionally different symbiotic bacteria

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Organ-on-Chip Technology for Aerobic Intestinal Host – Anaerobic Microbiota Research

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Gut-on-a-Chip for the Analysis of Bacteria–Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet–Microbiota Relationship?

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In silico encounters: harnessing metabolic modelling to understand plant–microbe interactions

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Targeting the gut to prevent and counteract metabolic disorders and pathologies during aging

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Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics

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Meta‐Omics‐ and Metabolic Modeling‐Assisted Deciphering of Human Microbiota Metabolism

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Evolutionary Stability of Salmonella Competition with the Gut Microbiota: How the Environment Fosters Heterogeneity in Exploitative and Interference Competition

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Molecular systems biology approaches to investigate mechanisms of gut−brain communication in neurological diseases

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A Quantitative Systems Pharmacology Model Describing the Cellular Kinetic‐Pharmacodynamic Relationship for a Live Biotherapeutic Product to Support Microbiome Drug Development

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Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications

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Modelling the influence of vitamin D and probiotic supplementation on the microbiome and immune response

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

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A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets

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Quantitative modeling of human metabolism: A call for a community effort

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2′-Fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations

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Serum Metabolites Relate to Mucosal and Transmural Inflammation in Paediatric Crohn Disease

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Feeding the World Inside Us: Our Gut Microbiomes, Diet, and Health

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Systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosisPreprint

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Mapping out the gut microbiota-dependent trimethylamine N-oxide super pathway for systems biology applications

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Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models

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Gut Microbiome in Obesity Management

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Probiotics in mitigation of food allergies and lactose intolerance

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Engineering Microbial Biofilms for Improved Productivity of Biochemicals Important in Restoration of Degraded Ecosystems

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Bacterial biomarkers: new aspects of colorectal tumors diagnosis: reality or fantasy

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Microbiome Engineering towards Disease Therapy

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Gut Microbiota Shift in Obese Adolescents Born by Cesarean Section

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Microbial gatekeepers: unraveling the role of the gut microbiota enzyme DPP4 in diabetes management

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Molecular Mechanisms of Gut Microbiota–Immune System Crosstalk: From Mucosal Architecture to Adaptive Immunity Programming

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A multifaceted approach to harness probiotics as antagonists on plant based foods, for enhanced benefits to be reaped at a global level

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Microbiome: Current Status and Future Applications

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In‐depth characterization of genome‐scale network reconstructions for the in vitro synthesis in cell‐free systems

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Computational framework for exploring the interplay of diet and gut microbiota in autismPreprint

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Simulations of the infant gut microbiota suggest that complex ecological interactions regulate effects of human milk oligosaccharides on microbial mucin consumptionPreprint

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Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome

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

Bauer, E., & Thiele, I. (2018) · mSystems · doi:10.1128/msystems.00209-17 · Cited by 90 · see citing works

Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools

Altamirano, Á., Saa, P. A., & Garrido, D. A. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.035 · Cited by 25 · see citing works

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome

Manor, O., Levy, R., & Borenstein, E. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.07.021 · Cited by 81 · see citing works

Constraint-based modeling of host-microbe and microbe-microbe metabolic interactions in the human gut

Heinken, A. (2015) · Skemman

Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

Heinken, A., & Thiele, I. (2015) · Gut Microbes · doi:10.1080/19490976.2015.1023494 · Cited by 105 · see citing works