Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

(2021) Sonja Blasche et al.   Nature Microbiology

Polarization of microbial communities between competitive and cooperative metabolism

(2021) Daniel Machado et al.   Nature Ecology & Evolution

Clinically relevant mutations in core metabolic genes confer antibiotic resistance

(2021) Allison J. Lopatkin et al.   SCIENCE

Metabolic fitness landscapes predict the evolution of antibiotic resistance

(2021) Fernanda Pinheiro et al.   Nature Ecology & Evolution

Ultra-fast proteomics with Scanning SWATH

(2021) Christoph B. Messner et al.   NATURE BIOTECHNOLOGY

Drug resistance and tolerance in fungi

(2020) Judith Berman et al.   NATURE REVIEWS MICROBIOLOGY

Metabolic and genetic basis for auxotrophies in Gram-negative species

(2020) Yara Seif et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The microbial exometabolome: ecological resource and architect of microbial communities

(2020) Angela E. Douglas   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Metabolite sensing and signaling in Cancer

(2020) Yi-Ping Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cross-feeding modulates the rate and mechanism of antibiotic resistance evolution in a model microbial community of Escherichia coli and Salmonella enterica

(2020) Elizabeth M. Adamowicz et al.   PLoS Pathogens

Horizontal Gene Transfer as a Source of Conflict and Cooperation in Prokaryotes

(2020) Rebecca J. Hall et al.   Frontiers in Microbiology

Ecology and evolution of antimicrobial resistance in bacterial communities

(2020) Michael J. Bottery et al.   ISME Journal

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

Designing Metabolic Division of Labor in Microbial Communities

(2019) Meghan Thommes et al.   mSystems

A Laterally Transferred Viral Gene Modifies Aphid Wing Plasticity

(2019) Benjamin J. Parker et al.   CURRENT BIOLOGY

Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism

(2019) Viridiana Olin-Sandoval et al.   NATURE

Horizontal Gene Transfer and Its Association with Antibiotic Resistance in the Genus Aeromonas spp.

(2019) J. Manuel Bello-López et al.   Microorganisms

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev et al.   NATURE METHODS

Cross-feeding modulates antibiotic tolerance in bacterial communities

(2018) Elizabeth M. Adamowicz et al.   ISME Journal

Ecology and evolution of metabolic cross-feeding interactions in bacteria

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

The social network of microorganisms — how auxotrophies shape complex communities

(2018) Karsten Zengler et al.   NATURE REVIEWS MICROBIOLOGY

iPath3.0: interactive pathways explorer v3

(2018) Youssef Darzi et al.   NUCLEIC ACIDS RESEARCH

Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition

(2018) Jakob Vowinckel et al.   Scientific Reports

Community interactions and spatial structure shape selection on antibiotic resistant lineages

(2018) Sylvie Estrela et al.   PLoS Computational Biology

Metabolic capability and in situ activity of microorganisms in an oil reservoir

(2018) Yi-Fan Liu et al.   Microbiome

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts

(2018) Aleksej Zelezniak et al.   Cell Systems

Effect of aspartic acid and glutamate on metabolism and acid stress resistance of Acetobacter pasteurianus

(2017) Haisong Yin et al.   Microbial Cell Factories

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Elucidation of roles for vitamin B12in regulation of folate, ubiquinone, and methionine metabolism

(2017) Margaret F. Romine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic tolerance facilitates the evolution of resistance

(2017) Irit Levin-Reisman et al.   SCIENCE

The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites

(2017) Gerrit Wienhausen et al.   Frontiers in Microbiology

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

(2017) Olga Ponomarova et al.   Cell Systems

Cell-to-cell heterogeneity emerges as consequence of metabolic cooperation in a synthetic yeast community

(2016) Kate Campbell et al.   Biotechnology Journal

The Mechanistic Targets of Antifungal Agents: An Overview

(2016) Tryphon K. Mazu et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Cell-to-cell heterogeneity emerges as consequence of metabolic cooperation in a synthetic yeast community

(2016) Kate Campbell et al.   Biotechnology Journal

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

(2016) Octavio Perez-Garcia et al.   Frontiers in Microbiology

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

The metabolic background is a global player in Saccharomyces gene expression epistasis

(2016) Mohammad Tauqeer Alam et al.   Nature Microbiology

Nutrient-Sensing Mechanisms across Evolution

(2015) Lynne Chantranupong et al.   CELL

MitoLoc: A method for the simultaneous quantification of mitochondrial network morphology and membrane potential in single cells

(2015) Jakob Vowinckel et al.   MITOCHONDRION

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

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ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Long-term social dynamics drive loss of function in pathogenic bacteria

(2015) Sandra Breum Andersen 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

Improved initialisation of model-based clustering using Gaussian hierarchical partitions

(2015) Luca Scrucca et al.   Advances in Data Analysis and Classification

Self-establishing communities enable cooperative metabolite exchange in a eukaryote

(2015) Kate Campbell et al.   eLife

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

What do drug transporters really do?

(2014) Sanjay K. Nigam   NATURE REVIEWS DRUG DISCOVERY

MFS transporters required for multidrug/multixenobiotic (MD/MX) resistance in the model yeast: understanding their physiological function through post-genomic approaches

(2014) Sandra C. dos Santos et al.   Frontiers in Physiology

Improved Blue, Green, and Red Fluorescent Protein Tagging Vectors for S. cerevisiae

(2013) Sidae Lee et al.   PLoS One

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome

(2013) Michael R. Gillings   Frontiers in Microbiology

Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network inThermotoga maritima

(2012) Irina A. Rodionova et al.   ENVIRONMENTAL MICROBIOLOGY

Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

(2012) Nicole Paczia et al.   Microbial Cell Factories

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

An integrated approach to characterize genetic interaction networks in yeast metabolism

(2011) Balázs Szappanos et al.   NATURE GENETICS

Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection

(2011) Yo Suzuki et al.   NATURE METHODS

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Mixed-Culture Transcriptome Analysis Reveals the Molecular Basis of Mixed-Culture Growth in Streptococcus thermophilus and Lactobacillus bulgaricus

(2010) S. Sieuwerts et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Principles of early drug discovery

(2010) JP Hughes et al.   BRITISH JOURNAL OF PHARMACOLOGY

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Achieving Optimal Growth through Product Feedback Inhibition in Metabolism

(2010) Sidhartha Goyal et al.   PLoS Computational Biology