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

A third gyrovirus species in human faeces

(2012) T. G. Phan et al.   JOURNAL OF GENERAL VIROLOGY

Metagenomic Analysis of Viruses from Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China

(2012) Xingyi Ge et al.   JOURNAL OF VIROLOGY

Hypervariable loci in the human gut virome

(2012) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid diversification of coevolving marine Synechococcus and a virus

(2012) M. F. Marston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The importance of entering cells, non-trivial solutions for serious viruses

(2012) Gabriella Campadelli Fiume et al.   Current Opinion in Virology

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

(2012) Nathan L. Yozwiak et al.   PLoS Neglected Tropical Diseases

Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA

(2011) Rachel Marine et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

The next generation of bacteriophage therapy

(2011) Timothy K Lu et al.   CURRENT OPINION IN MICROBIOLOGY

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

(2011) Margret E. Berg Miller et al.   ENVIRONMENTAL MICROBIOLOGY

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

Unbiased Parallel Detection of Viral Pathogens in Clinical Samples by Use of a Metagenomic Approach

(2011) J. Yang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years

(2011) T. F. F. Ng et al.   JOURNAL OF GENERAL VIROLOGY

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 Virome of Pigs on a High-Density Farm

(2011) T. Shan et al.   JOURNAL OF VIROLOGY

The crisis of no new antibiotics—what is the way forward?

(2011) Laura JV Piddock   LANCET INFECTIOUS DISEASES

Viral metagenome analysis to guide human pathogen monitoring in environmental samples

(2011) K. Bibby et al.   LETTERS IN APPLIED MICROBIOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

The good viruses: viral mutualistic symbioses

(2011) Marilyn J. Roossinck   NATURE REVIEWS MICROBIOLOGY

Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes

(2011) Terry Fei Fan Ng et al.   PLoS One

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

(2011) Mart Krupovic et al.   PLoS One

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins

(2011) E. E. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

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

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Changes in Population Dynamics in Mutualistic versus Pathogenic Viruses

(2011) Marilyn Roossinck   Viruses-Basel

TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

(2011) Hernan A. Lorenzi et al.   Standards in Genomic Sciences

The Fecal Viral Flora of Wild Rodents

(2011) Tung G. Phan et al.   PLoS Pathogens

Metagenomic Analysis of Fever, Thrombocytopenia and Leukopenia Syndrome (FTLS) in Henan Province, China: Discovery of a New Bunyavirus

(2011) Bianli Xu et al.   PLoS Pathogens

Is the Genetic Landscape of the Deep Subsurface Biosphere Affected by Viruses?

(2011) Rika E. Anderson et al.   Frontiers in Microbiology

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages

(2010) C. Andrews-Pfannkoch et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Success of Self-Administered Home Fecal Transplantation for Chronic Clostridium difficile Infection

(2010) Michael S. Silverman et al.   Clinical Gastroenterology and Hepatology

Human Bocaviruses Are Highly Diverse, Dispersed, Recombination Prone, and Prevalent in Enteric Infections

(2010) Amit Kapoor et al.   JOURNAL OF INFECTIOUS DISEASES

Metagenomic Analysis of the Viromes of Three North American Bat Species: Viral Diversity among Different Bat Species That Share a Common Habitat

(2010) E. F. Donaldson et al.   JOURNAL OF VIROLOGY

Bat Guano Virome: Predominance of Dietary Viruses from Insects and Plants plus Novel Mammalian Viruses

(2010) L. Li et al.   JOURNAL OF VIROLOGY

Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study

(2010) Karthikeyan K Kumarasamy et al.   LANCET INFECTIOUS DISEASES

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

(2010) D. Willner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

(2010) P. J. Turnbaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard

(2010) Beatrix Coetzee et al.   VIROLOGY

Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber

(2009) Lejla Pašić et al.   BMC GENOMICS

Redefining Chronic Viral Infection

(2009) Herbert W. Virgin et al.   CELL

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

SYNTHESIS: Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence

(2009) Sam P. Brown et al.   Evolutionary Applications

Multiple novel astrovirus species in human stool

(2009) A. Kapoor et al.   JOURNAL OF GENERAL VIROLOGY

Novel circular DNA viruses in stool samples of wild-living chimpanzees

(2009) O. Blinkova et al.   JOURNAL OF GENERAL VIROLOGY

Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis

(2009) J. G. Victoria et al.   JOURNAL OF VIROLOGY

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

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

(2009) Shota Nakamura et al.   PLoS One

Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy

(2009) T. K. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism

(2009) K. M. Oliver et al.   SCIENCE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli

(2009) Marietta Weiss et al.   VIROLOGY

Human stool contains a previously unrecognized diversity of novel astroviruses

(2009) Stacy R Finkbeiner et al.   Virology Journal

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Virus infection improves drought tolerance

(2008) Ping Xu et al.   NEW PHYTOLOGIST

Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa

(2008) R. L. Vega Thurber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral diversity and dynamics in an infant gut

(2008) Mya Breitbart et al.   RESEARCH IN MICROBIOLOGY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Identification of a novel picornavirus related to cosaviruses in a child with acute diarrhea

(2008) Lori R Holtz et al.   Virology Journal

Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

(2008) Stacy R. Finkbeiner et al.   PLoS Pathogens