Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco et al.   Nature Communications

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

(2019) Laurent Heirendt et al.   Nature Protocols

Modeling trophic dependencies and exchanges among insects’ bacterial symbionts in a host-simulated environment

(2018) Itai Opatovsky et al.   BMC GENOMICS

Modeling metabolism of the human gut microbiome

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

Ecology and evolution of metabolic cross-feeding interactions in bacteria

(2018) Glen D'Souza et al.   NATURAL PRODUCT REPORTS

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

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

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

(2018) Morgan N. Price et al.   PLoS Genetics

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Quorum Sensing Modulates the Epibiotic-Parasitic Relationship Between Actinomyces odontolyticus and Its Saccharibacteria epibiont, a Nanosynbacter lyticus Strain, TM7x

(2018) Joseph K. Bedree et al.   Frontiers in Microbiology

Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host

(2018) Batbileg Bor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Unculturability and the Formation of Intercellular Metabolic Networks

(2017) Samay Pande et al.   TRENDS IN MICROBIOLOGY

Genome-scale metabolic models applied to human health and disease

(2017) Daniel J Cook et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

(2017) Matthew B. Biggs et al.   PLoS Computational Biology

Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates

(2017) Christopher Jacobs et al.   PLoS One

Enumeration of minimal stoichiometric precursor sets in metabolic networks

(2016) Ricardo Andrade et al.   Algorithms for Molecular Biology

Metabolic shifts and structural changes in the gut microbiota upon branched-chain amino acid supplementation in middle-aged mice

(2016) Zhan Yang et al.   AMINO ACIDS

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

First Cultivation of Health-Associated Tannerella sp. HOT-286 (BU063)

(2016) S.R. Vartoukian et al.   JOURNAL OF DENTAL RESEARCH

Synthetic Ecology of Microbes: Mathematical Models and Applications

(2016) Ali R. Zomorrodi et al.   JOURNAL OF MOLECULAR BIOLOGY

Heme Synthesis and Acquisition in Bacterial Pathogens

(2016) Jacob E. Choby et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli

(2016) Daniel C Sévin et al.   NATURE METHODS

A practical guide to the oral microbiome and its relation to health and disease

(2016) K Krishnan et al.   ORAL DISEASES

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

In Vitro Cultivation of ‘Unculturable’ Oral Bacteria, Facilitated by Community Culture and Media Supplementation with Siderophores

(2016) Sonia R. Vartoukian et al.   PLoS One

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

(2015) Brian J. Vaccaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

(2015) Roie Levy et al.   BMC BIOINFORMATICS

Metabolic interactions in microbial communities: untangling the Gordian knot

(2015) Olga Ponomarova et al.   CURRENT OPINION IN MICROBIOLOGY

Oral Microbiome Metabolism

(2015) N. Takahashi   JOURNAL OF DENTAL RESEARCH

Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces

(2015) Batbileg Bor et al.   MICROBIAL ECOLOGY

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

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

Metabolic network modeling of microbial communities

(2015) Matthew B. Biggs et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Metabolic cross-feeding via intercellular nanotubes among bacteria

(2015) Samay Pande et al.   Nature Communications

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Single Cell Genomics of Uncultured, Health-Associated Tannerella BU063 (Oral Taxon 286) and Comparison to the Closely Related Pathogen Tannerella forsythia

(2014) Clifford J. Beall et al.   PLoS One

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

(2014) P. Jorth et al.   mBio

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

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

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

(2014) Raphy Zarecki et al.   PLoS Computational Biology

The phenomenon of microbial uncultivability

(2013) SS Epstein   CURRENT OPINION IN MICROBIOLOGY

Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes

(2013) J. J. Davis et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Microbial metabolic exchange in 3D

(2013) Jeramie D Watrous et al.   ISME Journal

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Multiple Single-Cell Genomes Provide Insight into Functions of Uncultured Deltaproteobacteria in the Human Oral Cavity

(2013) Alisha G. Campbell et al.   PLoS One

Metabolic Proximity in the Order of Colonization of a Microbial Community

(2013) Varun Mazumdar et al.   PLoS One

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

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases

(2013) José F. Siqueira Jr et al.   Journal of Oral Microbiology

NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species

(2012) Anat Kreimer et al.   BIOINFORMATICS

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment

(2012) R. Carr et al.   BIOINFORMATICS

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

Covalently linked polyamines in the cell wall peptidoglycan of the anaerobes belonging to the order Selenomonadales

(2012) Koei Hamana et al.   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

Engineering ecosystems and synthetic ecologies

(2012) Michael T. Mee et al.   Molecular BioSystems

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Microbial metabolic exchange—the chemotype-to-phenotype link

(2011) Vanessa V Phelan et al.   Nature Chemical Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

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

Oral multispecies biofilm development and the key role of cell–cell distance

(2010) Paul E. Kolenbrander et al.   NATURE REVIEWS MICROBIOLOGY

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Applications of genome-scale metabolic reconstructions

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

Metabolic-network-driven analysis of bacterial ecological strategies

(2009) Shiri Freilich et al.   GENOME BIOLOGY

Lipid domains in bacterial membranes and the action of antimicrobial agents

(2008) Richard M. Epand et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Teichoic acids and related cell-wall glycopolymers in Gram-positive physiology and host interactions

(2008) Christopher Weidenmaier et al.   NATURE REVIEWS MICROBIOLOGY

Cascading failure and robustness in metabolic networks

(2008) A. G. Smart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosynthetic Potentials of Metabolites and Their Hierarchical Organization

(2008) Franziska Matthäus et al.   PLoS Computational Biology

An environmental perspective on metabolism

(2007) Thomas Handorf et al.   JOURNAL OF THEORETICAL BIOLOGY