The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection

Understanding the Complex Phage-Host Interactions in Biofilm Communities

(2021) Diana P. Pires et al.   Annual Review of Virology

Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals

(2021) Joshua M. Kirsch et al.   Annual Review of Virology

Intestinal Bacteriophage Therapy: Looking for Optimal Efficacy

(2021) François Javaudin et al.   CLINICAL MICROBIOLOGY REVIEWS

Systematic exploration of Escherichia coli phage–host interactions with the BASEL phage collection

(2021) Enea Maffei et al.   PLOS BIOLOGY

Compilation of Escherichia coli K-12 outer membrane phage receptors - their function and some historical remarks

(2020) Klaus Hantke   FEMS MICROBIOLOGY LETTERS

New insights into intestinal phages

(2020) R. Sausset et al.   Mucosal Immunology

Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages

(2020) Aurélie Mathieu et al.   Nature Communications

The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages

(2020) Marta Lourenço et al.   Cell Host & Microbe

Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

(2020) Jorge A. M. de Sousa et al.   ISME Journal

Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization

(2020) Tao Zuo et al.   Cell Host & Microbe

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Bacterial, viral and parasitic pathogens analysed by qPCR: Findings from a prospective study of travellers’ diarrhoea

(2020) Tinja Lääveri et al.   Travel Medicine and Infectious Disease

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model

(2019) Bryan B. Hsu et al.   Cell Host & Microbe

Transcription factor YcjW controls the emergency H2S production in E. coli

(2019) Lyly Luhachack et al.   Nature Communications

Impact of bile salts on coevolutionary dynamics between the gut bacterium Escherichia coli and its lytic phage PP01

(2019) John G. Scanlan et al.   INFECTION GENETICS AND EVOLUTION

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Bacterial biodiversity drives the evolution of CRISPR-based phage resistance

(2019) Ellinor O. Alseth et al.   NATURE

The pan-immune system of bacteria: antiviral defence as a community resource

(2019) Aude Bernheim et al.   NATURE REVIEWS MICROBIOLOGY

The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition

(2019) Jeffrey K. Cornuault et al.   ISME Journal

The Diversity of Bacterial Lifestyles Hampers Bacteriophage Tenacity

(2018) Marta Lourenço et al.   Viruses-Basel

Leaky resistance and the conditions for the existence of lytic bacteriophage

(2018) Waqas N. Chaudhry et al.   PLOS BIOLOGY

H2S, a Bacterial Defense Mechanism against the Host Immune Response

(2018) Tracy Toliver-Kinsky et al.   INFECTION AND IMMUNITY

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Ménage à trois in the human gut: interactions between host, bacteria and phages

(2017) Mohammadali Khan Mirzaei et al.   NATURE REVIEWS MICROBIOLOGY

Inflammation boosts bacteriophage transfer between Salmonella spp.

(2017) Médéric Diard et al.   SCIENCE

The Human Gut Phage Community and Its Implications for Health and Disease

(2017) Pilar Manrique et al.   Viruses-Basel

Enteroaggregative Escherichia coli Adherence Fimbriae Drive Inflammatory Cell Recruitment via Interactions with Epithelial MUC1

(2017) Erik J. Boll et al.   mBio

Phage Inhibit Pathogen Dissemination by Targeting Bacterial Migrants in a Chronic Infection Model

(2017) Sophie E. Darch et al.   mBio

Dynamic biofilm architecture confers individual and collective mechanisms of viral protection

(2017) Lucia Vidakovic et al.   Nature Microbiology

Links between Transcription, Environmental Adaptation and Gene Variability inEscherichia coli: Correlations between Gene Expression and Gene Variability Reflect Growth Efficiencies

(2016) Jean-Paul Feugeas et al.   MOLECULAR BIOLOGY AND EVOLUTION

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Quorum Regulated Resistance of Vibrio cholerae against Environmental Bacteriophages

(2016) M. Mozammel Hoque et al.   Scientific Reports

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

(2016) Marta Lourenço et al.   PLoS Genetics

Next-Generation “-omics” Approaches Reveal a Massive Alteration of Host RNA Metabolism during Bacteriophage Infection of Pseudomonas aeruginosa

(2016) Anne Chevallereau et al.   PLoS Genetics

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data

(2016) Hugo Varet et al.   PLoS One

Carnitine in bacterial physiology and metabolism

(2015) Jamie A. Meadows et al.   MICROBIOLOGY-SGM

The outer mucus layer hosts a distinct intestinal microbial niche

(2015) Hai Li et al.   Nature Communications

Bacteriophage T4 can produce progeny virions in extremely slowly growingEscherichia colihost: comparison of a mathematical model with the experimental data

(2014) Piotr Golec et al.   FEMS MICROBIOLOGY LETTERS

Phenotypic Resistance and the Dynamics of Bacterial Escape from Phage Control

(2014) James J. Bull et al.   PLoS One

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

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

PredictingIn VivoEfficacy of Therapeutic Bacteriophages Used To Treat Pulmonary Infections

(2013) Marine Henry et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Identification and Characterization of a Novel Flagellum-Dependent Salmonella-Infecting Bacteriophage, iEPS5

(2013) Y. Choi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron

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

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Population and Evolutionary Dynamics of Phage and Bacteria with CRISPR–Mediated Immunity

(2013) Bruce R. Levin et al.   PLoS Genetics

Virulent Bacteriophages Can Target O104:H4 Enteroaggregative Escherichia coli in the Mouse Intestine

(2012) Damien Maura et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Receptor Diversity and Host Interaction of Bacteriophages Infecting Salmonella enterica Serovar Typhimurium

(2012) Hakdong Shin et al.   PLoS One

Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice

(2011) Damien Maura et al.   ENVIRONMENTAL MICROBIOLOGY

Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content

(2010) Yolande Bertin et al.   ENVIRONMENTAL MICROBIOLOGY

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular mechanisms of Escherichia coli pathogenicity

(2009) Matthew A. Croxen et al.   NATURE REVIEWS MICROBIOLOGY

In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli

(2009) Marietta Weiss et al.   VIROLOGY

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Stochastic Receptor Expression Allows Sensitive Bacteria to Evade Phage Attack. Part I: Experiments

(2008) E. Chapman-McQuiston et al.   BIOPHYSICAL JOURNAL

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine

(2008) A. J. Fabich et al.   INFECTION AND IMMUNITY