Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems

Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa

(2020) Xingya Zhou et al.   BMC GENOMICS

Targeting of temperate phages drives loss of type I CRISPR–Cas systems

(2020) Clare Rollie et al.   NATURE

Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

(2020) Shuo Wang et al.   Genes

Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches

(2020) Yan Jia et al.   Genes

Role of enterotoxigenic Escherichia coli (ETEC) prophage in spreading antibiotic resistance in a porcine‐derived environment

(2020) Mianzhi Wang et al.   ENVIRONMENTAL MICROBIOLOGY

More than Simple Parasites: the Sociobiology of Bacteriophages and Their Bacterial Hosts

(2020) Patrick R. Secor et al.   mBio

Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation

(2020) Qiuxiang Zhang et al.   Genes

Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae

(2020) Ines Bleriot et al.   Microbial Genomics

Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium

(2020) Meichen Pan et al.   Microorganisms

Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects

(2020) Dan Huang et al.   Food Bioscience

Identification, characterization, and phylogenetic analysis of eight new inducible prophages in Lactobacillus

(2020) Zhangming Pei et al.   VIRUS RESEARCH

Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

(2020) Zhiqiu Yin et al.   mSystems

Prophages are associated with extensive CRISPR–Cas auto-immunity

(2020) Franklin L Nobrega et al.   NUCLEIC ACIDS RESEARCH

Dietary Fructose and Microbiota-Derived Short-Chain Fatty Acids Promote Bacteriophage Production in the Gut Symbiont Lactobacillus reuteri

(2019) Jee-Hwan Oh et al.   Cell Host & Microbe

Prophage induction, but not production of phage particles, is required for lethal disease in a microbiome-replete murine model of enterohemorrhagic E. coli infection

(2019) Sowmya Balasubramanian et al.   PLoS Pathogens

Yet More Evidence of Collusion: a New Viral Defense System Encoded by Gordonia Phage CarolAnn

(2019) Matthew T. Montgomery et al.   mBio

Isolation and Characterization of Lactobacillus brevis Phages

(2019) Feyereisen et al.   Viruses-Basel

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

(2019) Guilhem Faure et al.   NATURE REVIEWS MICROBIOLOGY

Temperate Bacteriophages from Chronic Pseudomonas aeruginosa Lung Infections Show Disease-Specific Changes in Host Range and Modulate Antimicrobial Susceptibility

(2019) Mohammad A. Tariq et al.   mSystems

Antibiotic Resistance of LACTOBACILLUS Strains

(2019) Elizaveta A. Anisimova et al.   CURRENT MICROBIOLOGY

Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage

(2019) Matthew A. Nethery et al.   BMC GENOMICS

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis

(2019) Reza Rezaei Javan et al.   Nature Communications

Biodiversity and Classification of Phages Infecting Lactobacillus brevis

(2019) Marine Feyereisen et al.   Frontiers in Microbiology

Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model

(2018) Ferdi L Hellweger et al.   ISME Journal

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Systematic discovery of antiphage defense systems in the microbial pangenome

(2018) Shany Doron et al.   SCIENCE

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

(2018) Walid Mottawea et al.   Frontiers in Microbiology

Molecular mechanisms of CRISPR–Cas spacer acquisition

(2018) Jon McGinn et al.   NATURE REVIEWS MICROBIOLOGY

Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli

(2018) Alexandra B. Crawley et al.   Scientific Reports

Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp.

(2018) Ilenia Campedelli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prediction of the intestinal resistome by a three-dimensional structure-based method

(2018) Etienne Ruppé et al.   Nature Microbiology

Less effective selection leads to larger genomes

(2017) Tristan Lefébure et al.   GENOME RESEARCH

Lysogeny in nature: mechanisms, impact and ecology of temperate phages

(2017) Cristina Howard-Varona et al.   ISME Journal

Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends

(2017) Moslem Papizadeh et al.   MICROBIAL PATHOGENESIS

Generalist species drive microbial dispersion and evolution

(2017) Sira Sriswasdi et al.   Nature Communications

Detecting Lactococcus lactis Prophages by Mitomycin C-Mediated Induction Coupled to Flow Cytometry Analysis

(2017) Joana Oliveira et al.   Frontiers in Microbiology

Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica

(2017) Anna Colavecchio et al.   Frontiers in Microbiology

DISARM is a widespread bacterial defence system with broad anti-phage activities

(2017) Gal Ofir et al.   Nature Microbiology

Pneumococcal prophages are diverse, but not without structure or history

(2017) Angela B. Brueggemann et al.   Scientific Reports

Characterization of prophages of Lactococcus garvieae

(2017) Giovanni Eraclio et al.   Scientific Reports

Prophages of the genusBifidobacteriumas modulating agents of the infant gut microbiota

(2016) Gabriele Andrea Lugli et al.   ENVIRONMENTAL MICROBIOLOGY

Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis

(2016) Zhenshun Zeng et al.   ISME Journal

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Comparative analysis of prophage-like elements inHelicobactersp. genomes

(2016) Xiangyu Fan et al.   PeerJ

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

(2016) C. Monard et al.   Scientific Reports

IBS: an illustrator for the presentation and visualization of biological sequences: Fig. 1.

(2015) Wenzhong Liu et al.   BIOINFORMATICS

Tackling antibiotic resistance: the environmental framework

(2015) Thomas U. Berendonk et al.   NATURE REVIEWS MICROBIOLOGY

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

(2015) Zhihong Sun et al.   Nature Communications

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

(2015) Welkin H Pope et al.   eLife

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

Comparative genome-scale analysis of niche-based stress-responsive genes in Lactobacillus helveticus strains

(2014) Suja Senan et al.   GENOME

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting

(2014) Gregory W. Goldberg et al.   NATURE

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

(2014) Pedro H. Oliveira et al.   NUCLEIC ACIDS RESEARCH

HemI: A Toolkit for Illustrating Heatmaps

(2014) Wankun Deng et al.   PLoS One

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

Remarkable Mechanisms in Microbes to Resist Phage Infections

(2014) Ron L. Dy et al.   Annual Review of Virology

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

(2014) Jennifer R Huddleston   Infection and Drug Resistance

Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Human Fecal Samples

(2013) Pablo Quirós et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Characterization of the Genome of the Dairy Lactobacillus helveticus Bacteriophage ΦAQ113

(2013) Miriam Zago et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity

(2013) Tamara Smokvina et al.   PLoS One

Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation

(2012) Jeff R Broadbent et al.   BMC GENOMICS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Sequence analysis of the Lactobacillus temperate phage Sha1

(2011) Bo Hyun Yoon et al.   ARCHIVES OF VIROLOGY

Genome analysis of Lactobacillus fermentum temperate bacteriophage ФPYB5

(2010) Xiuhong Zhang et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA