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

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

Communication between viruses guides lysis–lysogeny decisions

(2017) Zohar Erez et al.   NATURE

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

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

Bacteria–Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality

(2017) Pauline D. Scanlan   TRENDS IN MICROBIOLOGY

Simulation of the M13 life cycle I: Assembly of a genetically-structured deterministic chemical kinetic simulation

(2017) Steven W. Smeal et al.   VIROLOGY

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

(2017) Martial Marbouty et al.   Science Advances

Analysis of the Intestinal Microbiome of a Recovered Clostridium difficile Patient after Fecal Transplantation

(2017) Felix Broecker et al.   DIGESTION

Long-term microbiota and virome in a Zürich patient after fecal transplantation againstClostridium difficileinfection

(2016) Felix Broecker et al.   Annals of the New York Academy of Sciences

An evaluation of the therapeutic potential of fecal microbiota transplantation to treat infectious and metabolic diseases

(2016) Albert K Groen et al.   EMBO Molecular Medicine

Prophages of the genusBifidobacteriumas modulating agents of the infant gut microbiota

(2016) Gabriele Andrea Lugli et al.   ENVIRONMENTAL MICROBIOLOGY

Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice

(2016) Min-Soo Kim et al.   ENVIRONMENTAL MICROBIOLOGY

Lytic to temperate switching of viral communities

(2016) B. Knowles 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

Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation

(2016) Christel Chehoud et al.   mBio

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Fecal Transplants: What Is Being Transferred?

(2016) Diana P. Bojanova et al.   PLOS BIOLOGY

Hyperexpansion of RNA Bacteriophage Diversity

(2016) Siddharth R. Krishnamurthy et al.   PLOS BIOLOGY

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

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

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

(2016) M. P. Francino   Frontiers in Microbiology

Transmission of viruses via our microbiomes

(2016) Melissa Ly et al.   Microbiome

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

(2015) Jason M. Norman et al.   CELL

The Virome in Host Health and Disease

(2015) Ken Cadwell   IMMUNITY

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

(2015) Benjamin Bolduc et al.   ISME Journal

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

(2015) Adina Howe et al.   ISME Journal

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

(2015) Jennifer R Brum et al.   ISME Journal

Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model

(2015) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Coevolution with Bacteriophages Drives Genome-Wide Host Evolution and Constrains the Acquisition of Abiotic-Beneficial Mutations

(2015) Pauline D. Scanlan 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

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time

(2015) Britt Koskella et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

(2015) Hyun Jung Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

(2015) Jeremy J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Gut microbiota and aging

(2015) P. W. OToole et al.   SCIENCE

Viral Transmission Dynamics at Single-Cell Resolution Reveal Transiently Immune Subpopulations Caused by a Carrier State Association

(2015) William Cenens et al.   PLoS Genetics

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

(2015) Simon Roux et al.   eLife

The human urine virome in association with urinary tract infections

(2015) Tasha M. Santiago-Rodriguez et al.   Frontiers in Microbiology

The human gut virome: a multifaceted majority

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

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Fecal microbiota transplantation: in perspective

(2015) Shaan Gupta et al.   Therapeutic Advances in Gastroenterology

Chemostat culture systems support diverse bacteriophage communities from human feces

(2015) Tasha M. Santiago-Rodriguez et al.   Microbiome

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

(2015) Josué L. Castro-Mejía et al.   Microbiome

Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure

(2015) Sarah M. Bahr et al.   EBioMedicine

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes

(2015) Shira R. Abeles et al.   PLoS One

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

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Metagenomic analysis of double-stranded DNA viruses in healthy adults

(2014) Kristine M Wylie et al.   BMC BIOLOGY

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

(2014) Susana Fuentes et al.   ISME Journal

Classification and quantification of bacteriophage taxa in human gut metagenomes

(2014) Alison S Waller et al.   ISME Journal

Expanding the Role of the Virome: Commensalism in the Gut

(2014) Ken Cadwell   JOURNAL OF VIROLOGY

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting

(2014) Gregory W. Goldberg et al.   NATURE

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

(2014) Lesley Hoyles et al.   RESEARCH IN MICROBIOLOGY

Exploiting gut bacteriophages for human health

(2014) Marion Dalmasso et al.   TRENDS IN MICROBIOLOGY

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

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

Bacteriophages: an underestimated role in human and animal health?

(2014) Marianne De Paepe et al.   Frontiers in Cellular and Infection Microbiology

Viruses and the Microbiota

(2014) Christopher M. Robinson et al.   Annual Review of Virology

CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

(2013) Rotem Sorek et al.   Annual Review of Biochemistry

Phage-induced diversification improves host evolvability

(2013) Hywel TP Williams   BMC EVOLUTIONARY BIOLOGY

Association between living environment and human oral viral ecology

(2013) Refugio Robles-Sikisaka et al.   ISME Journal

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Resident viruses and their interactions with the immune system

(2013) Breck A Duerkop et al.   NATURE IMMUNOLOGY

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Holding a grudge

(2013) Eran Mick et al.   RNA Biology

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences

(2013) Lesley A. Ogilvie et al.   Nature Communications

The global virome: not as big as we thought?

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

Microbiota's 'little helpers': bacteriophages and antibiotic-associated responses in the gut microbiome

(2013) Christine L Sun et al.   GENOME BIOLOGY

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

(2013) Elaine O Petrof et al.   Microbiome

Virulent Bacteriophages Can Target O104:H4 Enteroaggregative Escherichia coli in the Mouse Intestine

(2012) Damien Maura et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

(2012) Fredrik Bäckhed et al.   Cell Host & Microbe

Transfer of Intestinal Microbiota From Lean Donors Increases Insulin Sensitivity in Individuals With Metabolic Syndrome

(2012) Anne Vrieze et al.   GASTROENTEROLOGY

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

(2012) Joe Bondy-Denomy et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

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

A composite bacteriophage alters colonization by an intestinal commensal bacterium

(2012) B. A. Duerkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VIROME: a standard operating procedure for analysis of viral metagenome sequences

(2012) K. Eric Wommack et al.   Standards in Genomic Sciences

Metagenomics and future perspectives in virus discovery

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

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

Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice

(2011) Damien Maura et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) S. Minot et al.   GENOME RESEARCH

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

(2011) Mart Krupovic et al.   PLoS One

Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection

(2010) Lanying Zeng et al.   CELL

Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

The Escherichia coli CRISPR System Protects from   Lysogenization, Lysogens, and Prophage Induction

(2010) R. Edgar et al.   JOURNAL OF BACTERIOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

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

Explaining microbial population genomics through phage predation

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

Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases

(2008) Daniel A. Peterson et al.   Cell Host & Microbe

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

(2008) P Lepage et al.   GUT

Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?

(2008) John H Paul   ISME Journal

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

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

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Viral diversity and dynamics in an infant gut

(2008) Mya Breitbart et al.   RESEARCH IN MICROBIOLOGY

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY