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

Reef invertebrate viromics: diversity, host specificity and functional capacity

(2018) Patrick W. Laffy et al.   ENVIRONMENTAL MICROBIOLOGY

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx ( Lynx canadensis ), moose ( Alces alces ) and snowshoe hare ( Lepus americanus ) inhabiting the Colorado San Juan Mountains

(2018) Simona Kraberger et al.   INFECTION GENETICS AND EVOLUTION

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China

(2018) Dan-Ting Yu et al.   JOURNAL OF SOILS AND SEDIMENTS

Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection

(2018) Mirela D’arc et al.   Retrovirology

Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity

(2018) Eric C. Keen et al.   TRENDS IN MICROBIOLOGY

The gut virome of the protochordate model organism, Ciona intestinalis subtype A

(2018) Brittany A. Leigh et al.   VIRUS RESEARCH

Enteric Virome Sensing—Its Role in Intestinal Homeostasis and Immunity

(2018) Rebecca Metzger et al.   Viruses-Basel

Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community

(2018) Chinmay V. Tikhe et al.   Frontiers in Microbiology

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan

(2018) Mitsuhiro Yoshida et al.   Frontiers in Microbiology

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

(2018) Angela McCann et al.   PeerJ

The gut virome: a neglected actor in colon cancer pathogenesis

(2017) Dinesh Kumar Dahiya   Future Microbiology

Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome

(2017) Tao Zuo et al.   GUT

Diversity and Distribution Characteristics of Viruses in Soils of a Marine-Terrestrial Ecotone in East China

(2017) Dan-Ting Yu et al.   MICROBIAL ECOLOGY

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Virus–host interactions and their roles in coral reef health and disease

(2017) Rebecca Vega Thurber et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

(2017) Elliot J Lefkowitz et al.   NUCLEIC ACIDS RESEARCH

Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics

(2017) Paloma S. Moreno et al.   PLoS One

How to Name and Classify Your Phage: An Informal Guide

(2017) Evelien Adriaenssens et al.   Viruses-Basel

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

(2017) Pilar Manrique et al.   Viruses-Basel

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils

(2017) Li-Li Han et al.   Scientific Reports

Aquarium Viromes: Viromes of Human-Managed Aquatic Systems

(2017) Yiseul Kim et al.   Frontiers in Microbiology

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

(2017) Natalya Yutin et al.   Nature Microbiology

Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae

(2017) Lianghua Guo et al.   VIROLOGICA SINICA

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

(2016) Matthew J. Neave et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

(2016) Benjamin Bolduc et al.   ISME Journal

Healthy human gut phageome

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

The Bacterial Microbiome and Virome Milestones of Infant Development

(2016) Efrem S. Lim et al.   TRENDS IN MICROBIOLOGY

The microviridae: Diversity, assembly, and experimental evolution

(2016) Sarah M. Doore et al.   VIROLOGY

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Generation of Germ-Free Ciona intestinalis for Studies of Gut-Microbe Interactions

(2016) Brittany A. Leigh et al.   Frontiers in Microbiology

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts

(2016) Lars Schreiber et al.   Frontiers in Microbiology

Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant

(2016) Victoria M. Pearson et al.   PeerJ

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

(2016) Simon Roux et al.   PeerJ

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

(2016) Kevin R. Theis et al.   mSystems

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

(2015) Brian Reavy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2015) Jason M. Norman et al.   CELL

The human gut microbiota and virome: Potential therapeutic implications

(2015) Emidio Scarpellini et al.   DIGESTIVE AND LIVER DISEASE

A novel sister clade to the enterobacteria microviruses (familyMicroviridae) identified in methane seep sediments

(2015) Samuel Joseph Bryson et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2015) Efrem S Lim et al.   NATURE MEDICINE

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

(2015) Alejandro Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and diversity of ssDNA Microviridae viruses in two peri-alpine lakes (Annecy and Bourget, France)

(2015) Xu Zhong et al.   RESEARCH IN MICROBIOLOGY

Gut microbiota and aging

(2015) P. W. OToole et al.   SCIENCE

A novel, highly divergent ssDNA virus identified in Brazil infecting apple, pear and grapevine

(2015) Marcos Fernando Basso et al.   VIRUS RESEARCH

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

(2015) Jon G. Sanders et al.   Nature Communications

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment

(2015) Jessica M. Labonté et al.   Frontiers in Microbiology

Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands

(2015) Achim Quaiser et al.   Frontiers in Microbiology

The human gut virome: a multifaceted majority

(2015) Lesley A. Ogilvie et al.   Frontiers in Microbiology

Identification and genomic analysis of a novel member of Microviridae, IME-16, through high-throughput sequencing

(2015) Peng Shu et al.   VIROLOGICA SINICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Classification and quantification of bacteriophage taxa in human gut metagenomes

(2014) Alison S Waller et al.   ISME Journal

Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein

(2014) Max Hopkins et al.   ISME Journal

Faecal virome of cats in an animal shelter

(2014) W. Zhang et al.   JOURNAL OF GENERAL VIROLOGY

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota

(2014) Larry J. Dishaw et al.   PLoS One

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation

(2014) Brejnev Muhizi Muhire et al.   PLoS One

Previously unknown and highly divergent ssDNA viruses populate the oceans

(2013) Jessica M Labonté et al.   ISME Journal

Metagenomic Analysis of Viral Communities in (Hado)Pelagic Sediments

(2013) Mitsuhiro Yoshida et al.   PLoS One

Metagenomic Analysis of the Ferret Fecal Viral Flora

(2013) Saskia L. Smits 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

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Confined aquifers as viral reservoirs

(2013) Renee J. Smith et al.   Environmental Microbiology Reports

Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea

(2013) Jessica M. Labonté et al.   Frontiers in Microbiology

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta)

(2012) K. Rosario et al.   JOURNAL OF GENERAL VIROLOGY

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

(2012) Simon Roux et al.   PLoS One

Evolution and Diversity of the Microviridae Viral Family through a Collection of 81 New Complete Genomes Assembled from Virome Reads

(2012) Simon Roux et al.   PLoS One

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

The intestinal microbiome of the pig

(2012) Richard Isaacson et al.   ANIMAL HEALTH RESEARCH REVIEWS

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

(2011) Kyoung-Ho Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metavir: a web server dedicated to virome analysis

(2011) Simon Roux et al.   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

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

(2011) S. Minot et al.   GENOME RESEARCH

Metagenomic Analysis of the Viral Flora of Pine Marten and European Badger Feces

(2011) J. M. A. van den Brand et al.   JOURNAL OF VIROLOGY

The Fecal Viral Flora of California Sea Lions

(2011) L. Li et al.   JOURNAL OF VIROLOGY

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

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

Microviridae Goes Temperate: Microvirus-Related Proviruses Reside in the Genomes of Bacteroidetes

(2011) Mart Krupovic et al.   PLoS One

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

(2010) Kimberly P Tucker et al.   ISME Journal

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Metagenomic analysis of viruses in reclaimed water

(2009) Karyna Rosario et al.   ENVIRONMENTAL MICROBIOLOGY

Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater

(2009) Orr H Shapiro et al.   ISME Journal

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

High Diversity of the Viral Community from an Antarctic Lake

(2009) A. Lopez-Bueno et al.   SCIENCE

Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

(2008) K.-H. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biodiversity and biogeography of phages in modern stromatolites and thrombolites

(2008) Christelle Desnues et al.   NATURE

Viral diversity and dynamics in an infant gut

(2008) Mya Breitbart et al.   RESEARCH IN MICROBIOLOGY