Infection trains the host for microbiota-enhanced resistance to pathogens

Long-Term Effects of Early-Life Antibiotic Exposure on Resistance to Subsequent Bacterial Infection

(2020) Claire Roubaud-Baudron et al.   mBio

Metabolism the Difficile Way: The Key to the Success of the Pathogen Clostridioides difficile

(2019) Meina Neumann-Schaal et al.   Frontiers in Microbiology

A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia

(2019) Spencer C. Peck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

The ancestral and industrialized gut microbiota and implications for human health

(2019) Erica D. Sonnenburg et al.   NATURE REVIEWS MICROBIOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Laboratory mice born to wild mice have natural microbiota and model human immune responses

(2019) Stephan P. Rosshart et al.   SCIENCE

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis

(2019) Jeffrey R. Singer et al.   NATURE MEDICINE

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

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

Temporal development of the gut microbiome in early childhood from the TEDDY study

(2018) Christopher J. Stewart et al.   NATURE

Mouse Genome Database (MGD) 2019

(2018) Carol J Bult et al.   NUCLEIC ACIDS RESEARCH

White Adipose Tissue Is a Reservoir for Memory T Cells and Promotes Protective Memory Responses to Infection

(2017) Seong-Ji Han et al.   IMMUNITY

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens

(2017) Sohn Kim et al.   IMMUNOLOGICAL REVIEWS

Comprehensive Arrayed Transposon Mutant Library of Klebsiella pneumoniae Outbreak Strain KPNIH1

(2017) Beth Ramage et al.   JOURNAL OF BACTERIOLOGY

Mechanisms of bile acid mediated inflammation in the liver

(2017) Man Li et al.   MOLECULAR ASPECTS OF MEDICINE

Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis

(2017) Wei Jia et al.   Nature Reviews Gastroenterology & Hepatology

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis

(2017) Franziska Faber et al.   PLoS Pathogens

The path towards microbiome-based metabolite treatment

(2017) Jotham Suez et al.   Nature Microbiology

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 and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease

(2016) Karishma Kamdar et al.   Cell Host & Microbe

Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response

(2016) Tiffany A. Reese et al.   Cell Host & Microbe

Host Selection of Microbiota via Differential Adhesion

(2016) Kirstie McLoughlin et al.   Cell Host & Microbe

Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

(2016) Annika Wahlström et al.   Cell Metabolism

Normalizing the environment recapitulates adult human immune traits in laboratory mice

(2016) Lalit K. Beura et al.   NATURE

The design and analysis of transposon insertion sequencing experiments

(2016) Michael C. Chao et al.   NATURE REVIEWS MICROBIOLOGY

Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration

(2016) C. A. Lopez et al.   SCIENCE

Helminth infection promotes colonization resistance via type 2 immunity

(2016) Deepshika Ramanan et al.   SCIENCE

Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization

(2016) Sean Conlan et al.   mBio

A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration

(2016) Apollo Stacy et al.   mBio

The Terminal Oxidase Cytochrome bd Promotes Sulfide-resistant Bacterial Respiration and Growth

(2016) Elena Forte et al.   Scientific Reports

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel

(2015) Neelendu Dey et al.   CELL

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling

(2015) Maayan Levy et al.   CELL

Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity

(2015) Denise Morais da Fonseca et al.   CELL

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identification of a probiotic bacteria-derived activator of the aryl hydrocarbon receptor that inhibits colitis

(2014) Suguru Fukumoto et al.   IMMUNOLOGY AND CELL BIOLOGY

Fecal microbiota transplantation: effectiveness, complexities and lingering concerns

(2014) E G Pamer   Mucosal Immunology

Enterohepatic bacterial infections dysregulate the FGF15-FGFR4 endocrine axis

(2013) Guillaume Romain et al.   BMC MICROBIOLOGY

Intraluminal Containment of Commensal Outgrowth in the Gut during Infection-Induced Dysbiosis

(2013) Michael J. Molloy et al.   Cell Host & Microbe

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Effective T-cell recall responses require the taurine transporter Taut

(2012) Susanne Kaesler et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries

(2011) Andrew L Goodman et al.   Nature Protocols

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A murine model of urinary tract infection

(2009) Chia-Suei Hung et al.   Nature Protocols

ExplorEnz: the primary source of the IUBMB enzyme list

(2008) A. G. McDonald et al.   NUCLEIC ACIDS RESEARCH