Deciphering Active Prophages from Metagenomes

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

(2021) Kristopher Kieft et al.   Nature Communications

Virus-associated organosulfur metabolism in human and environmental systems

(2021) Kristopher Kieft et al.   Cell Reports

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Fitness benefits to bacteria of carrying prophages and prophage‐encoded antibiotic‐resistance genes peak in different environments

(2020) Carolin C. Wendling et al.   EVOLUTION

Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

(2020) Manuel Kleiner et al.   Microbiome

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Prophage Hunter: an integrative hunting tool for active prophages

(2019) Wenchen Song et al.   NUCLEIC ACIDS RESEARCH

Nitrogen sourcing during viral infection of marine cyanobacteria

(2019) Jacob R. Waldbauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryptic prophage-encoded small protein protects Escherichia coli from phage infection by inhibiting inner membrane receptor proteins

(2019) Preethi T. Ragunathan et al.   JOURNAL OF BACTERIOLOGY

Resistance in marine cyanobacteria differs against specialist and generalist cyanophages

(2019) Sophia Zborowsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome

(2019) Andrew J. Gasparrini et al.   Nature Microbiology

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

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

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

(2019) Amy E. Zimmerman et al.   NATURE REVIEWS MICROBIOLOGY

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

Lysogeny is prevalent and widely distributed in the murine gut microbiota

(2018) Min-Soo Kim et al.   ISME Journal

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

Prophage-driven genomic structural changes promote Bartonella vertical evolution

(2018) Ricardo Gutiérrez et al.   Genome Biology and Evolution

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

(2018) Andrey N. Shkoporov et al.   Nature Communications

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

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

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

A Clostridioides difficile bacteriophage genome encodes functional binary toxin-associated genes

(2017) Thomas Riedel et al.   JOURNAL OF BIOTECHNOLOGY

Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients

(2017) Qing He et al.   GigaScience

Prophage-mediated defence against viral attack and viral counter-defence

(2017) Rebekah M. Dedrick et al.   Nature Microbiology

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred

(2017) Umer Zeeshan Ijaz et al.   PLoS One

Stability of active prophages in industrial Lactococcus lactis strains in the presence of heat, acid, osmotic, oxidative and antibiotic stressors

(2016) Chun-Hoong Ho et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

The Escherichia coli Cryptic Prophage Protein YfdR Binds to DnaA and Initiation of Chromosomal Replication Is Inhibited by Overexpression of the Gene Cluster yfdQ-yfdR-yfdS-yfdT

(2016) Yasunori Noguchi et al.   Frontiers in Microbiology

Phage-mediated horizontal gene transfer of both prophage and heterologous DNA by ϕBB-1, a bacteriophage ofBorrelia burgdorferi

(2016) Christian H. Eggers et al.   Pathogens and Disease

Emerging Roles of Hydrogen Sulfide in Inflammatory and Neoplastic Colonic Diseases

(2016) Fang-Fang Guo et al.   Frontiers in Physiology

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Bacteriophage lambda: Early pioneer and still relevant

(2015) Sherwood R. Casjens et al.   VIROLOGY

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Genome-Based Identification of Active Prophage Regions by Next Generation Sequencing in Bacillus licheniformis DSM13

(2015) Robert Hertel et al.   PLoS One

Iron Triggers λSo Prophage Induction and Release of Extracellular DNA in Shewanella oneidensis MR-1 Biofilms

(2014) Lucas Binnenkade et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Classification and quantification of bacteriophage taxa in human gut metagenomes

(2014) Alison S Waller et al.   ISME Journal

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

(2011) Ole Skovgaard et al.   GENOME RESEARCH

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

(2010) Nianzhi Jiao et al.   NATURE REVIEWS MICROBIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Prophage Spontaneous Activation Promotes DNA Release Enhancing Biofilm Formation in Streptococcus pneumoniae

(2010) Margarida Carrolo et al.   PLoS One

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Endogenous and Exogenous Hydrogen Sulfide Promotes Resolution of Colitis in Rats

(2009) John L. Wallace et al.   GASTROENTEROLOGY