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

Fermented Foods as Experimentally Tractable Microbial Ecosystems

(2015) Benjamin E. Wolfe et al.   CELL

The activated sludge ecosystem contains a core community of abundant organisms

(2015) Aaron M Saunders et al.   ISME Journal

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

The demographic determinants of human microbiome health

(2015) Sylvie Estrela et al.   TRENDS IN MICROBIOLOGY

Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations

(2015) Albertas Janulevicius et al.   PLoS Computational Biology

Association of Biodiversity with the Rates of Micropollutant Biotransformations among Full-Scale Wastewater Treatment Plant Communities

(2014) David R. Johnson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Modelling the emergent dynamics and major metabolites of the human colonic microbiota

(2014) Helen Kettle et al.   ENVIRONMENTAL MICROBIOLOGY

Evolution of species interactions determines microbial community productivity in new environments

(2014) Francesca Fiegna et al.   ISME Journal

Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms

(2014) Jordi van Gestel et al.   ISME Journal

A thermodynamic theory of microbial growth

(2014) Elie Desmond-Le Quéméner et al.   ISME Journal

War and peace: social interactions in infections

(2014) H. C. Leggett et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Characterization of spiraling patterns in spatial rock-paper-scissors games

(2014) Bartosz Szczesny et al.   PHYSICAL REVIEW E

Erosion of functional independence early in the evolution of a microbial mutualism

(2014) K. L. Hillesland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluvial network organization imprints on microbial co-occurrence networks

(2014) S. Widder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

(2014) David Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

(2014) J. J. Faith et al.   Science Translational Medicine

Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations

(2014) O. Eilam et al.   mBio

Cooperative secretions facilitate host range expansion in bacteria

(2014) Luke McNally et al.   Nature Communications

Clustering in community structure across replicate ecosystems following a long-term bacterial evolution experiment

(2014) Hasan Celiker et al.   Nature Communications

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

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

A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

(2014) Natacha Bodenhausen et al.   PLoS Genetics

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Historical contingency in species interactions: towards niche-based predictions

(2013) Rachel L. Vannette et al.   ECOLOGY LETTERS

Real-time microbial adaptive diversification in soil

(2013) Pedro Gómez et al.   ECOLOGY LETTERS

Linking thermodynamics and kinetics to assess pathway reversibility in anaerobic bioprocesses

(2013) Rebeca González-Cabaleiro et al.   Energy & Environmental Science

Community history affects the predictability of microbial ecosystem development

(2013) Eulyn Pagaling et al.   ISME Journal

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Spatial self-organization favors heterotypic cooperation over cheating

(2013) Babak Momeni et al.   eLife

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Towards synthetic microbial consortia for bioprocessing

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

Geomicrobial Kinetics: Extrapolating Laboratory Studies to Natural Environments

(2012) Qusheng Jin et al.   GEOMICROBIOLOGY JOURNAL

Engineering ecosystems and synthetic ecologies

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

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Localized cell death focuses mechanical forces during 3D patterning in a biofilm

(2012) M. Asally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations

(2012) O. X. Cordero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological Populations of Bacteria Act as Socially Cohesive Units of Antibiotic Production and Resistance

(2012) O. X. Cordero et al.   SCIENCE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Early microbial succession in redeveloping dental biofilms in periodontal health and disease

(2011) F. R. Teles et al.   JOURNAL OF PERIODONTAL RESEARCH

Dynamic model of flexible phytoplankton nutrient uptake

(2011) J. A. Bonachela 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

Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico

(2011) Kalin Vetsigian et al.   PLOS BIOLOGY

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation

(2010) Jessica R. Sieber et al.   Annual Review of Microbiology

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature

(2010) Vincent J Denef et al.   ISME Journal

Mathematical modelling of carbohydrate degradation by human colonic microbiota

(2010) Rafael Muñoz-Tamayo et al.   JOURNAL OF THEORETICAL BIOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

The large-scale organization of the bacterial network of ecological co-occurrence interactions

(2010) Shiri Freilich et al.   NUCLEIC ACIDS RESEARCH

Microbial population dynamics by digital in-line holographic microscopy

(2010) Zak Frentz et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Mathematical Description of Microbial Biofilms

(2010) Isaac Klapper et al.   SIAM REVIEW

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play

(2009) D. M. Post et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

(2008) Ainslie E.F. Little et al.   Annual Review of Microbiology

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

(2008) T. Kosaka et al.   GENOME RESEARCH

Self-organization of mobile populations in cyclic competition

(2008) Tobias Reichenbach et al.   JOURNAL OF THEORETICAL BIOLOGY