E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source

Establishing causality in Salmonella-microbiota-host interaction: the use of gnotobiotic mouse models and synthetic microbial communities

(2021) Bärbel Stecher   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities

(2020) Claudia Eberl et al.   Frontiers in Microbiology

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition

(2020) Rita A. Oliveira et al.   Nature Microbiology

Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice

(2020) Bidong D. Nguyen et al.   Cell Host & Microbe

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production

(2020) Lisa Osbelt et al.   PLoS Pathogens

Salmonella versus the Microbiome

(2020) Andrew W. L. Rogers et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection

(2019) Eric M. Velazquez et al.   Nature Microbiology

Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis

(2019) Simone Herp et al.   Cell Host & Microbe

Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice

(2019) Sandra Y. Wotzka et al.   Nature Microbiology

A protocol to evaluate RNA sequencing normalization methods

(2019) Zachary B. Abrams et al.   BMC BIOINFORMATICS

Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes

(2018) Blanca Taboada et al.   BIOINFORMATICS

A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection

(2018) Amanda Jacobson et al.   Cell Host & Microbe

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

(2018) Yara Seif et al.   Nature Communications

The global burden and epidemiology of invasive non-typhoidal Salmonella infections

(2018) Ruchita Balasubramanian et al.   Human Vaccines & Immunotherapeutics

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus

(2018) Matthew E. Mokszycki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria

(2017) Ana Sousa et al.   MOLECULAR BIOLOGY AND EVOLUTION

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data

(2017) Marius Vital et al.   mSystems

Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes

(2017) Matthew L. Jenior et al.   mSystems

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella

(2016) Fabian Rivera-Chávez et al.   Cell Host & Microbe

Genetic Characterization of the Galactitol Utilization Pathway of Salmonella enterica Serovar Typhimurium

(2016) Nicoletta Nolle et al.   JOURNAL OF BACTERIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Microcins mediate competition among Enterobacteriaceae in the inflamed gut

(2016) Martina Sassone-Corsi et al.   NATURE

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

(2016) Sandrine Brugiroux et al.   Nature Microbiology

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography–tandem mass spectrometry

(2015) Jun Han et al.   ANALYTICA CHIMICA ACTA

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

(2015) Hiroshi Tsugawa et al.   NATURE METHODS

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

(2015) Alyxandria M. Schubert et al.   mBio

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Microbiota-Derived Hydrogen Fuels Salmonella Typhimurium Invasion of the Gut Ecosystem

(2013) Lisa Maier et al.   Cell Host & Microbe

Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron

(2013) Elisa Deriu et al.   Cell Host & Microbe

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Streptomycin-Induced Inflammation Enhances Escherichia coli Gut Colonization Through Nitrate Respiration

(2013) A. M. Spees et al.   mBio

Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals

(2013) Roy R. Chaudhuri et al.   PLoS Genetics

The Streptomycin-Treated Mouse Intestine SelectsEscherichia coli envZMissense Mutants That Interact with Dense and Diverse Intestinal Microbiota

(2012) Mary P. Leatham-Jensen et al.   INFECTION AND IMMUNITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

(2012) B. Stecher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

(2012) C. Kroger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

The Global Burden of NontyphoidalSalmonellaGastroenteritis

(2010) Shannon E. Majowicz et al.   CLINICAL INFECTIOUS DISEASES

Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria

(2010) Bärbel Stecher et al.   PLoS Pathogens

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS