THOR’s Hammer: the Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community

A Chemical Counterpunch: Chromobacterium violaceum ATCC 31532 Produces Violacein in Response to Translation-Inhibiting Antibiotics

(2020) Gabriel L. Lozano et al.   mBio

Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior

(2019) Gabriel L. Lozano et al.   mBio

Transcriptomic mechanism of a phytohormone 6-benzylaminopurine (6-BAP) stimulating lipid and DHA synthesis in Aurantiochytrium sp.

(2019) Xinjun Yu et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Bacterial analogs of plant tetrahydropyridine alkaloids mediate microbial interactions in a rhizosphere model system

(2019) Gabriel L. Lozano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Experimental Microbiomes: Models Not to Scale

(2019) Marc G. Chevrette et al.   mSystems

Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes

(2019) Natalia Gutiérrez et al.   mSystems

Advances and Challenges in Metatranscriptomic Analysis

(2019) Migun Shakya et al.   Frontiers in Genetics

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2018)   BIOINFORMATICS

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead

(2018) Benjamin E. Wolfe   mSystems

Emerging evolutionary paradigms in antibiotic discovery

(2018) Marc G. Chevrette et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Changes in the genetic requirements for microbial interactions with increasing community complexity

(2018) Manon Morin et al.   eLife

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

(2018) Kevin D'hoe et al.   eLife

Temperate phages as self-replicating weapons in bacterial competition

(2017) Xiang-Yi Li et al.   Journal of the Royal Society Interface

Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria

(2017) Paul A. Jensen et al.   Cell Reports

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

(2017) Olga Ponomarova et al.   Cell Systems

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

(2017) John L. Chodkowski et al.   mSystems

Temperate phages enhance pathogen fitness in chronic lung infection

(2016) Emily V Davies et al.   ISME Journal

Multifaceted Interfaces of Bacterial Competition

(2016) Reed M. Stubbendieck et al.   JOURNAL OF BACTERIOLOGY

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

(2016) Erik K. Kastman et al.   mBio

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community

(2016) Xiaokan Guo et al.   PLoS Computational Biology

Bacterial Communities: Interactions to Scale

(2016) Reed M. Stubbendieck et al.   Frontiers in Microbiology

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality

(2016) Yue Jiang et al.   Microbiome

Differential transcriptional response to antibiotics byPseudomonas putida DOT-T1E

(2015) Carlos Molina-Santiago et al.   ENVIRONMENTAL MICROBIOLOGY

Combinatorial code governing cellular responses to complex stimuli

(2015) Antonio Cappuccio et al.   Nature Communications

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity

(2014) Benjamin E. Wolfe et al.   CELL

Escherichia coli protein YgiD produces the structural unit of plant pigments betalains: characterization of a prokaryotic enzyme with DOPA-extradiol-dioxygenase activity

(2013) Fernando Gandía-Herrero et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2013) Karen De Roy et al.   ENVIRONMENTAL MICROBIOLOGY

Antibiotics at subinhibitory concentrations improve the quorum sensing behavior ofChromobacterium violaceum

(2013) Zhanjun Liu et al.   FEMS MICROBIOLOGY LETTERS

Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm

(2013) Kai Wei Kelvin Lee et al.   ISME Journal

High-Throughput Screening of Multispecies Biofilm Formation and Quantitative PCR-Based Assessment of Individual Species Proportions, Useful for Exploring Interspecific Bacterial Interactions

(2013) Dawei Ren et al.   MICROBIAL ECOLOGY

Competition sensing: the social side of bacterial stress responses

(2013) Daniel M. Cornforth et al.   NATURE REVIEWS MICROBIOLOGY

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR

(2012) Gottfried J. Palm et al.   NUCLEIC ACIDS RESEARCH

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

(2012) P. Nicolas et al.   SCIENCE

In vitro multispecies Lubbock chronic wound biofilm model

(2010) Yan Sun et al.   WOUND REPAIR AND REGENERATION

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Antibiotics as signals that trigger specific bacterial responses

(2008) Alicia Fajardo et al.   CURRENT OPINION IN MICROBIOLOGY

Genome-wide responses to carbonyl electrophiles inBacillus subtilis: control of the thiol-dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR-family regulator YraB (AdhR)

(2008) Nguyen Thi Thu Huyen et al.   MOLECULAR MICROBIOLOGY

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