Metabolic dependencies drive species co-occurrence in diverse microbial communities

Synthetic microbial communities

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

Niche engineering demonstrates a latent capacity for fungal-algal mutualism

(2014) E. F. Y. Hom et al.   SCIENCE

The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem

(2014) William Inskeep   Frontiers in Microbiology

Metabolic activity and symbiotic interactions of lactic acid bacteria and yeasts isolated from water kefir

(2013) Jasmin Stadie et al.   FOOD MICROBIOLOGY

A latent capacity for evolutionary innovation through exaptation in metabolic systems

(2013) Aditya Barve et al.   NATURE

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

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

Evolutionary history predicts the stability of cooperation in microbial communities

(2013) Alexandre Jousset et al.   Nature Communications

Rethinking Community Assembly through the Lens of Coexistence Theory

(2012) J. HilleRisLambers et al.   Annual Review of Ecology Evolution and Systematics

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

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

Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

(2012) Nicole Paczia et al.   Microbial Cell Factories

Deciphering a global network of functionally associated post-translational modifications

(2012) Pablo Minguez et al.   Molecular Systems Biology

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

Microbial communities in natural and disturbed peatlands: A review

(2012) R. Andersen et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

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

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

(2010) Lance D Miller et al.   BMC MICROBIOLOGY

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron 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

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

AQUA: automated quality improvement for multiple sequence alignments

(2009) J. Muller et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

Network Relationships of Bacteria in a Stable Mixed Culture

(2008) Souichiro Kato et al.   MICROBIAL ECOLOGY