Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

(2020) John Beaulaurier et al.   GENOME RESEARCH

Implications of bacteriophages on the acquisition and spread of antibiotic resistance in the environment

(2020) José Luis Balcázar   INTERNATIONAL MICROBIOLOGY

Phage-specific metabolic reprogramming of virocells

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

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

(2020) Kira Moon et al.   Microbiome

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

(2020) Shao-Ming Gao et al.   Microbiome

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

(2020) Kristopher Kieft et al.   Microbiome

Errors in long-read assemblies can critically affect protein prediction

(2019) Mick Watson et al.   NATURE BIOTECHNOLOGY

Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

(2019) Fuyong Li et al.   Microbiome

Cyanophage MazG is a pyrophosphohydrolase but unable to hydrolyse magic spot nucleotides

(2019) Branko Rihtman et al.   Environmental Microbiology Reports

Riding the wave of genomics to investigate aquatic coliphage diversity and activity

(2019) Slawomir Michniewski et al.   ENVIRONMENTAL MICROBIOLOGY

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins

(2019) J. Leonardo Moreno-Gallego et al.   Cell Host & Microbe

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

(2019) Joanna Warwick-Dugdale et al.   PeerJ

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Viruses as key reservoirs of antibiotic resistance genes in the environment

(2019) Didier Debroas et al.   ISME Journal

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

(2019) Robert A. Edwards et al.   Nature Microbiology

Discovery and characterization of the evolution, variation and functions of diversity-generating retroelements using thousands of genomes and metagenomes

(2019) Fazhe Yan et al.   BMC GENOMICS

Studying the gut virome in the metagenomic era: challenges and perspectives

(2019) Sanzhima Garmaeva et al.   BMC BIOLOGY

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

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

Detecting contamination in viromes using ViromeQC

(2019) Moreno Zolfo et al.   NATURE BIOTECHNOLOGY

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

(2019) Reza Rezaei Javan et al.   Nature Communications

Gut Bacteriophage: Current Understanding and Challenges

(2019) Thomas D. S. Sutton et al.   Frontiers in Endocrinology

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Exploring the Genomic Traits of Non-toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile

(2018) Daniel Castillo et al.   Frontiers in Microbiology

PNGM-1, a Novel Subclass B3 Metallo-β-Lactamase from a Deep-Sea Sediment Metagenome

(2018) Kwang Seung Park et al.   Journal of Global Antimicrobial Resistance

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean

(2018) Francisco Martinez-Hernandez et al.   ISME Journal

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

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

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

A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage

(2018) Sean Benler et al.   Microbiome

Exploring the contribution of bacteriophages to antibiotic resistance

(2017) Itziar Lekunberri et al.   ENVIRONMENTAL POLLUTION

Comparative Genomics of Bacteriophage of the Genus Seuratvirus

(2017) Pavelas Sazinas et al.   Genome Biology and Evolution

Marine microbiology: Algal virus boosts nitrogen uptake in the ocean

(2017) Ashley York   NATURE REVIEWS MICROBIOLOGY

Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey

(2017) Li Wu et al.   NUCLEIC ACIDS RESEARCH

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

(2017) Adam Monier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How to Name and Classify Your Phage: An Informal Guide

(2017) Evelien Adriaenssens et al.   Viruses-Basel

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Dietary energy drives the dynamic response of bovine rumen viral communities

(2017) Christopher L. Anderson et al.   Microbiome

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Sulfate reduction in microorganisms—recent advances and biotechnological applications

(2016) Christian Rückert   CURRENT OPINION IN MICROBIOLOGY

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2016) François Enault et al.   ISME Journal

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

A novel virulence-associated protein, vapE, in Streptococcus suis serotype 2

(2016) XUE JI et al.   Molecular Medicine Reports

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

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Production and management of cattle manure in the UK and implications for land application practice

(2016) K. A. Smith et al.   SOIL USE AND MANAGEMENT

Zonula occludens toxins and their prophages in Campylobacter species

(2016) Fang Liu et al.   Gut Pathogens

Phage-mediated Shiga toxin (Stx) horizontal gene transfer and expression in non-Shiga toxigenicEnterobacterandEscherichia colistrains

(2016) Rowaida K.S. Khalil et al.   Pathogens and Disease

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses

(2016) Simon Roux et al.   PeerJ

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

A Meta-analysis of Bacterial Diversity in the Feces of Cattle

(2015) Minseok Kim et al.   CURRENT MICROBIOLOGY

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

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

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

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Unexplained diarrhoea in HIV-1 infected individuals

(2014) Bas B Oude Munnink et al.   BMC INFECTIOUS DISEASES

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

The fate and biogeochemical cycling of viral elements

(2014) Rui Zhang et al.   NATURE REVIEWS MICROBIOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Environment

(2014) Jose Luis Balcazar   PLoS Pathogens

Evidence for metaviromic islands in marine phages

(2014) Carolina Megumi Mizuno et al.   Frontiers in Microbiology

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Importance of prophages to evolution and virulence of bacterial pathogens

(2013) Louis-Charles Fortier et al.   Virulence

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Environmental consequences of processing manure to produce mineral fertilizer and bio-energy

(2012) J.W. De Vries et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Comparative metagenomics of microbial traits within oceanic viral communities

(2011) Itai Sharon et al.   ISME Journal

Molecular Epidemiology of Mastitis Pathogens of Dairy Cattle and Comparative Relevance to Humans

(2011) Ruth N. Zadoks et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

(2010) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

LCA of comprehensive pig manure management incorporating integrated technology systems

(2010) Trakarn Prapaspongsa et al.   JOURNAL OF CLEANER PRODUCTION

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

T4 genes in the marine ecosystem: studies of the T4-like cyanophages and their role in marine ecology

(2010) Martha RJ Clokie et al.   Virology Journal

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence ofSynechococcushost genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution

(2009) Andrew D. Millard et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative Genomic Analysis of Ten Streptococcus pneumoniae Temperate Bacteriophages

(2009) P. Romero et al.   JOURNAL OF BACTERIOLOGY

Evaluation of the sulfate-reducing bacterial population associated with stored swine slurry

(2008) Kimberly L. Cook et al.   ANAEROBE

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Life cycle assessment of conventional and organic milk production in the Netherlands

(2007) M.A. Thomassen et al.   AGRICULTURAL SYSTEMS