Phage diversity, genomics and phylogeny

Megaphages infect Prevotella and variants are widespread in gut microbiomes

(2019) Audra E. Devoto et al.   Nature Microbiology

Structural dynamics of bacteriophage P22 infection initiation revealed by cryo-electron tomography

(2019) Chunyan Wang et al.   Nature Microbiology

Cryo-electron microscopy structure of the filamentous bacteriophage IKe

(2019) Jingwei Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis

(2019) Lasha Gogokhia 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

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

(2019) Jakub Barylski et al.   SYSTEMATIC BIOLOGY

The amazing HK97 fold: versatile results of modest differences

(2019) Robert L Duda et al.   Current Opinion in Virology

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

(2019) Simon Roux et al.   Nature Microbiology

Lysogeny is prevalent and widely distributed in the murine gut microbiota

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

ICTV Virus Taxonomy Profile: Plasmaviridae

(2018) Mart Krupovic et al.   JOURNAL OF GENERAL VIROLOGY

Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades

(2018) Anne Kupczok et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reproducible protocols for metagenomic analysis of human faecal phageomes

(2018) Andrey N. Shkoporov et al.   Microbiome

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

A Decade of Streptococcus thermophilus Phage Evolution in an Irish Dairy Plant

(2018) Katherine Lavelle et al.   APPLIED AND ENVIRONMENTAL 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

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

(2018) Kathryn M. Kauffman et al.   NATURE

Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta)

(2018) Alexandria Creasy et al.   Viruses-Basel

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

(2017) Robert M. Sinclair et al.   JOURNAL OF VIROLOGY

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

How to Name and Classify Your Phage: An Informal Guide

(2017) Evelien Adriaenssens et al.   Viruses-Basel

Viruses in the Oceanic Basement

(2017) Olivia D. Nigro et al.   mBio

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

(2017) Felipe H. Coutinho et al.   Nature Communications

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

(2017) Ravi K. Lokareddy et al.   Nature Communications

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

(2017) Mario López-Pérez et al.   PLoS Genetics

Viral communities of the human gut: metagenomic analysis of composition and dynamics

(2017) Varun Aggarwala et al.   Mobile DNA

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

Environmental drivers of viral community composition in Antarctic soils identified by viromics

(2017) Evelien M. Adriaenssens et al.   Microbiome

Bacteriophage evolution differs by host, lifestyle and genome

(2017) Travis N. Mavrich et al.   Nature Microbiology

Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species

(2016) Paula Szymczak et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

Genomic diversification of marine cyanophages into stable ecotypes

(2016) Marcia F. Marston et al.   ENVIRONMENTAL MICROBIOLOGY

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

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

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules

(2016) Pierre Legrand et al.   mBio

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

(2016) Jaime Iranzo et al.   mBio

Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ

(2016) Roman I Koning et al.   Nature Communications

Re-examination of the relationship between marine virus and microbial cell abundances

(2016) Charles H. Wigington et al.   Nature Microbiology

Piggyback-the-Winner in host-associated microbial communities

(2016) Cynthia B Silveira et al.   npj Biofilms and Microbiomes

To kill or not to kill: The balance between lytic and lysogenic viral infection is driven by trophic status

(2016) Jérôme P. Payet et al.   LIMNOLOGY AND OCEANOGRAPHY

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

(2015) Jason M. Norman et al.   CELL

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics

(2015) Jennifer R Brum et al.   ISME Journal

Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity

(2015) Graham F. Hatfull   JOURNAL OF VIROLOGY

The Kinetic and Thermodynamic Aftermath of Horizontal Gene Transfer Governs Evolutionary Recovery

(2015) Sarah M. Doore et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Efrem S Lim et al.   NATURE MEDICINE

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Environmental characteristics of Agulhas rings affect interocean plankton transport

(2015) E. Villar et al.   SCIENCE

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Nature׳s favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold

(2015) Margaret M. Suhanovsky et al.   VIROLOGY

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

Viruses in a 14th-Century Coprolite

(2014) S. Appelt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of different long-term fertilization regimes on the viral community in an agricultural soil of Southern China

(2014) Lin Chen et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

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

(2014) Bonnie L Hurwitz et al.   ISME Journal

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

A theoretical analysis of how strain-specific viruses can control microbial species diversity

(2014) T. F. Thingstad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of virus-like particles associated with the human faecal and caecal microbiota

(2014) Lesley Hoyles et al.   RESEARCH IN MICROBIOLOGY

Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

(2014) Julianne H. Grose et al.   VIROLOGY

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

(2014) T. C. Jordan et al.   mBio

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

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

Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages

(2014) Frazer J Rixon et al.   Current Opinion in Virology

Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases

(2014) Marianne De Paepe et al.   PLoS Genetics

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

(2013) Jennifer R Brum et al.   ISME Journal

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection

(2013) Lei Sun et al.   NATURE

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story

(2013) M. K. Pietila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Twelve previously unknown phage genera are ubiquitous in global oceans

(2013) K. Holmfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Plate Tectonics of Virus Shell Assembly and Reorganization in Phage Φ8, a Distant Relative of Mammalian Reoviruses

(2013) Kamel El Omari et al.   STRUCTURE

The global virome: not as big as we thought?

(2013) J Cesar Ignacio-Espinoza et al.   Current Opinion in Virology

Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery

(2013) Bibiana Peralta et al.   PLOS BIOLOGY

Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability

(2013) Louis-Marie Bobay et al.   PLoS Genetics

A suggested new bacteriophage genus: “Viunalikevirus”

(2012) Evelien M. Adriaenssens et al.   ARCHIVES OF VIROLOGY

A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

(2012) Geoffrey S Diemer et al.   Biology Direct

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

(2011) S. Minot et al.   GENOME RESEARCH

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

(2011) M. Krupovic et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genomic island variability facilitates Prochlorococcus–virus coexistence

(2011) Sarit Avrani et al.   NATURE

The DNA-packaging nanomotor of tailed bacteriophages

(2011) Sherwood R. Casjens   NATURE REVIEWS MICROBIOLOGY

Three-dimensional structure of a viral genome-delivery portal vertex

(2011) Adam S Olia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Phages have adapted the same protein fold to fulfill multiple functions in virion assembly

(2010) L. Cardarelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recombination and microdiversity in coastal marine cyanophages

(2009) Marcia F. Marston et al.   ENVIRONMENTAL MICROBIOLOGY

The Crystal Structure of Bacteriophage HK97 gp6: Defining a Large Family of Head–Tail Connector Proteins

(2009) Lia Cardarelli et al.   JOURNAL OF MOLECULAR BIOLOGY

The phage   major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system

(2009) L. G. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage genomics

(2008) Graham F Hatfull   CURRENT OPINION IN MICROBIOLOGY

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

(2008) P Lepage et al.   GUT

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

(2008) G. Lima-Mendez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage PM2

(2008) Nicola G.A. Abrescia et al.   MOLECULAR CELL

Virus evolution: how far does the double β-barrel viral lineage extend?

(2008) Mart Krupovič et al.   NATURE REVIEWS MICROBIOLOGY