Unraveling interactions in microbial communities - from co-cultures to microbiomes

Supplementation of Saturated Long-Chain Fatty Acids Maintains Intestinal Eubiosis and Reduces Ethanol-induced Liver Injury in Mice

(2015) Peng Chen et al.   GASTROENTEROLOGY

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Meta-analyses of human gut microbes associated with obesity and IBD

(2014) William A. Walters et al.   FEBS LETTERS

Host-Microbiome Interactions in Alcoholic Liver Disease

(2014) Peng Chen et al.   Gut and Liver

Dynamic flux balance analysis for synthetic microbial communities

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

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Comparative Proteomic Analysis of Experimental Evolution of the Bacillus cereus-Ketogulonicigenium vulgare Co-Culture

(2014) Qian Ma et al.   PLoS One

Metabolomic Analysis of Cooperative Adaptation between Co-Cultured Bacillus cereus and Ketogulonicigenium vulgare

(2014) Ming-Zhu Ding et al.   PLoS One

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Uranium removal and microbial community in a H 2 -based membrane biofilm reactor

(2014) Chen Zhou et al.   WATER RESEARCH

Prediction and quantification of bioactive microbiota metabolites in the mouse gut

(2014) Gautham V. Sridharan et al.   Nature Communications

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

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

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion

(2013) Diego Javier Jiménez et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

(2013) Timothy J Hanly et al.   Biotechnology for Biofuels

The Give and Take of Host-Microbe Symbioses

(2013) Nicole M. Gerardo   Cell Host & Microbe

Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

(2013) Karen De Roy et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

(2013) Mallory Embree et al.   ISME Journal

Inducing Secondary Metabolite Production by the Endophytic Fungus Fusarium tricinctum through Coculture with Bacillus subtilis

(2013) Antonius R. B. Ola et al.   JOURNAL OF NATURAL PRODUCTS

The plastic-associated microorganisms of the North Pacific Gyre

(2013) Henry S. Carson et al.   MARINE POLLUTION BULLETIN

Combinational expression of sorbose/sorbosone dehydrogenases and cofactor pyrroloquinoline quinone increases 2-keto-l-gulonic acid production in Ketogulonigenium vulgare–Bacillus cereus consortium

(2013) Jin Du et al.   METABOLIC ENGINEERING

Restoration of the gut microbial habitat as a disease therapy

(2013) David A Relman   NATURE BIOTECHNOLOGY

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

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

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

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

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

(2013) Harish Nagarajan et al.   Nature Communications

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

(2013) Haythem Latif et al.   PLoS Genetics

From Metabolism to Ecology: Cross-Feeding Interactions Shape the Balance between Polymicrobial Conflict and Mutualism

(2012) Sylvie Estrela et al.   AMERICAN NATURALIST

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Towards synthetic microbial consortia for bioprocessing

(2012) Jasmine Shong et al.   CURRENT OPINION IN BIOTECHNOLOGY

Competition between species can stabilize public-goods cooperation within a species

(2012) Hasan Celiker et al.   Molecular Systems Biology

A Programmable Escherichia coli Consortium via Tunable Symbiosis

(2012) Alissa Kerner et al.   PLoS One

Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome

(2012) Margaret L. Zupancic et al.   PLoS One

Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device

(2012) Seok Hoon Hong et al.   Nature Communications

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

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

Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures

(2011) Timothy J. Hanly et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Artificial construction and characterization of a fungal consortium that produces cellulolytic enzyme system with strong wheat straw saccharification

(2011) Hui Lin et al.   BIORESOURCE TECHNOLOGY

Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity

(2011) Hans C. Bernstein et al.   JOURNAL OF BIOTECHNOLOGY

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

(2011) Jan Schellenberger et al.   Nature Protocols

Cooperative Adaptation to Establishment of a Synthetic Bacterial Mutualism

(2011) Kazufumi Hosoda et al.   PLoS One

Integrated Proteomic and Metabolomic Analysis of an Artificial Microbial Community for Two-Step Production of Vitamin C

(2011) Qian Ma et al.   PLoS One

Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation

(2011) H.-W. Nutzmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures

(2010) Timothy J. Hanly et al.   BIOTECHNOLOGY AND BIOENGINEERING

An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure

(2010) Ivana Gudelj et al.   ECOLOGY LETTERS

Structural and operational complexity of the Geobacter sulfurreducens genome

(2010) Y. Qiu et al.   GENOME RESEARCH

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Creating and characterizing communities of human gut microbes in gnotobiotic mice

(2010) Jeremiah J Faith et al.   ISME Journal

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

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Emergent cooperation in microbial metabolism

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

An Environment-Sensitive Synthetic Microbial Ecosystem

(2010) Bo Hu et al.   PLoS One

Rapid evolution of stability and productivity at the origin of a microbial mutualism

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

Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria

(2010) Z. M. Summers et al.   SCIENCE

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Quorum Sensing Inhibition Selects for Virulence and Cooperation in Pseudomonas aeruginosa

(2010) Thilo Köhler et al.   PLoS Pathogens

Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) Bacteria in Acid Mine Drainage Biofilms

(2009) D. S. A. Goltsman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Global/temporal gene expression analysis of Escherichia coli in the early stages of symbiotic relationship development with the cellular slime mold Dictyostelium discoideum

(2009) Kumiko Kihara et al.   BIOSYSTEMS

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Central Role of the Cell in Microbial Ecology

(2009) K. Zengler   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans

(2009) V. Schroeckh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A synthetic Escherichia coli predator–prey ecosystem

(2008) Frederick K Balagaddé et al.   Molecular Systems Biology

Defined spatial structure stabilizes a synthetic multispecies bacterial community

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

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics

A co-fermentation strategy to consume sugar mixtures effectively

(2008) Mark A Eiteman et al.   Journal of Biological Engineering

New approach to optimize operational conditions for the biological treatment of a high-strength thiocyanate and ammonium waste: pH as key factor

(2007) Meiling Lay-Son et al.   WATER RESEARCH

Characterization of the loosely attached fraction of activated sludge bacteria

(2007) Fernando Morgan-Sagastume et al.   WATER RESEARCH