Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut

High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis and meningitis. A narrative review and clinical appraisal

(2019) Marie-Céline Zanella et al.   CLINICAL MICROBIOLOGY AND INFECTION

Phage Therapy in the Postantibiotic Era

(2019) Fernando L. Gordillo Altamirano et al.   CLINICAL MICROBIOLOGY REVIEWS

Choice of assembly software has a critical impact on virome characterisation

(2019) Thomas D. S. Sutton et al.   Microbiome

Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection

(2019) Johanna M. Sweere et al.   SCIENCE

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency

(2019) Juliana Siqueira et al.   Viruses-Basel

Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages

(2019) George Tetz et al.   Scientific Reports

The Intestinal Microbiota in Colorectal Cancer

(2018) Herbert Tilg et al.   CANCER CELL

Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

Inflammatory bowel disease and immunonutrition: novel therapeutic approaches through modulation of diet and the gut microbiome

(2018) Larissa S. Celiberto et al.   IMMUNOLOGY

The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients

(2018) Vyara Matson et al.   SCIENCE

Human Endogenous Retroviruses in Neurological Diseases

(2018) Patrick Küry et al.   TRENDS IN MOLECULAR MEDICINE

Virus–Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences

(2018) Matthew Moore et al.   Viruses-Basel

Shared and Distinct Features of Human Milk and Infant Stool Viromes

(2018) Pia S. Pannaraj et al.   Frontiers in Microbiology

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data

(2018) Saima Sultana Tithi et al.   PeerJ

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

(2018) Garold Fuks et al.   Microbiome

A human gut phage catalog correlates the gut phageome with type 2 diabetes

(2018) Yingfei Ma et al.   Microbiome

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses

(2018) Marcos Parras-Moltó et al.   Microbiome

Murine colitis reveals a disease-associated bacteriophage community

(2018) Breck A. Duerkop et al.   Nature Microbiology

Phage Therapy for a Multidrug-Resistant Acinetobacter baumannii Craniectomy Site Infection

(2018) Stephanie LaVergne et al.   Open Forum Infectious Diseases

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Spike-in genomic DNA for validating performance of metagenomics workflows

(2018) Arvind Venkataraman et al.   BIOTECHNIQUES

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohnʼs Disease

(2018) Melissa A. Fernandes et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Maximal viral information recovery from sequence data using VirMAP

(2018) Nadim J Ajami et al.   Nature Communications

Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet

(2018) Ravinder Nagpal et al.   Journal of Diabetes Research

Transkingdom network reveals bacterial players associated with cervical cancer gene expression program

(2018) Khiem Chi Lam et al.   PeerJ

Trends in Human Papillomavirus–Associated Cancers — United States, 1999–2015

(2018) Elizabeth A. Van Dyne et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Human polyomaviruses and cancer: an overview

(2018) JC Prado et al.   Clinics

Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial

(2018) Patrick Jault et al.   LANCET INFECTIOUS DISEASES

A novel variant of torque teno virus 7 identified in patients with Kawasaki disease

(2018) James B. Thissen et al.   PLoS One

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

(2018) Geoffrey D. Hannigan et al.   mBio

Microbial nutrient niches in the gut

(2017) Fátima C. Pereira et al.   ENVIRONMENTAL MICROBIOLOGY

Gut microbiota functions: metabolism of nutrients and other food components

(2017) Ian Rowland et al.   EUROPEAN JOURNAL OF NUTRITION

Gavage of Fecal Samples From Patients With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free and Conventional Mice

(2017) Sunny H. Wong et al.   GASTROENTEROLOGY

Lysogeny in nature: mechanisms, impact and ecology of temperate phages

(2017) Cristina Howard-Varona et al.   ISME Journal

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

(2017) Guoyan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

VirusSeeker, a computational pipeline for virus discovery and virome composition analysis

(2017) Guoyan Zhao et al.   VIROLOGY

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs

(2017) Yi Zheng et al.   VIROLOGY

Evolution of selective-sequencing approaches for virus discovery and virome analysis

(2017) Arvind Kumar et al.   VIRUS RESEARCH

Origins and challenges of viral dark matter

(2017) Siddharth R. Krishnamurthy et al.   VIRUS RESEARCH

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers

(2017) Sophie Nguyen et al.   mBio

Reduced microbial diversity in adult survivors of childhood acute lymphoblastic leukemia and microbial associations with increased immune activation

(2017) Ling Ling Chua et al.   Microbiome

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Bacteriophages as potential new mammalian pathogens

(2017) George V. Tetz et al.   Scientific Reports

ViromeScan: a new tool for metagenomic viral community profiling

(2016) Simone Rampelli et al.   BMC GENOMICS

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

(2016) Cynthia L. Monaco et al.   Cell Host & Microbe

Emerging Public Health Challenges of Shiga Toxin–ProducingEscherichia coliRelated to Changes in the Pathogen, the Population, and the Environment

(2016) Mohamed A. Karmali   CLINICAL INFECTIOUS DISEASES

Integration of the viral genome into the host cell genome: a double-edged sword

(2016) M. Pistello et al.   CLINICAL MICROBIOLOGY AND INFECTION

The Role of the Intestinal Microbiome in Type 1 Diabetes Pathogenesis

(2016) James C. Needell et al.   Current Diabetes Reports

Gut microbiome and lipid metabolism

(2016) Zheng Wang et al.   CURRENT OPINION IN LIPIDOLOGY

Prophages mediate defense against phage infection through diverse mechanisms

(2016) Joseph Bondy-Denomy et al.   ISME Journal

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Transkingdom control of viral infection and immunity in the mammalian intestine

(2016) J. K. Pfeiffer et al.   SCIENCE

The Bacterial Microbiome and Virome Milestones of Infant Development

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

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

(2016) M. P. Francino   Frontiers in Microbiology

Next generation sequencing data of a defined microbial mock community

(2016) Esther Singer et al.   Scientific Data

Human endogenous retroviruses and cancer

(2016) Gonzalez-Cao María et al.   Cancer Biology & Medicine

Piggyback-the-Winner in host-associated microbial communities

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

VIP: an integrated pipeline for metagenomics of virus identification and discovery

(2016) Yang Li et al.   Scientific Reports

Chemotherapy-driven dysbiosis in the intestinal microbiome

(2015) E. Montassier et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

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

(2015) Jason M. Norman et al.   CELL

Mammalian Lipopolysaccharide Receptors Incorporated into the Retroviral Envelope Augment Virus Transmission

(2015) Jessica Wilks et al.   Cell Host & Microbe

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Are human endogenous retroviruses triggers of autoimmune diseases? Unveiling associations of three diseases and viral loci

(2015) Bjørn A. Nexø et al.   IMMUNOLOGIC RESEARCH

Metagenomic Analysis of Crohnʼs Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers

(2015) Vicente Pérez-Brocal et al.   INFLAMMATORY BOWEL DISEASES

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

(2015) Efrem S Lim et al.   NATURE MEDICINE

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Human endogenous retrovirus-K contributes to motor neuron disease

(2015) Wenxue Li et al.   Science Translational Medicine

The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome

(2015) Geoffrey D. Hannigan et al.   mBio

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

The microbiome of uncontacted Amerindians

(2015) J. C. Clemente et al.   Science Advances

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data

(2015) Gordon M. Daly et al.   PLoS One

Review article: fungal microbiota and digestive diseases

(2014) Z. K. Wang et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

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

(2014) Simon Roux et al.   BMC BIOINFORMATICS

Bacterial Lipopolysaccharide Binding Enhances Virion Stability and Promotes Environmental Fitness of an Enteric Virus

(2014) Christopher M. Robinson et al.   Cell Host & Microbe

Human Astroviruses

(2014) Albert Bosch et al.   CLINICAL MICROBIOLOGY REVIEWS

Human oral viruses are personal, persistent and gender-consistent

(2014) Shira R Abeles et al.   ISME Journal

Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation

(2014) L. C. Osborne et al.   SCIENCE

Development of a virus detection and discovery pipeline using next generation sequencing

(2014) Thien Ho et al.   VIROLOGY

Altered Oral Viral Ecology in Association with Periodontal Disease

(2014) M. Ly et al.   mBio

Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Environment

(2014) Jose Luis Balcazar   PLoS Pathogens

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

Viruses and the Microbiota

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

Viral Carcinogenesis: Factors Inducing DNA Damage and Virus Integration

(2014) Yan Chen et al.   Cancers

Fusobacterium nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin/β-Catenin Signaling via its FadA Adhesin

(2013) Mara Roxana Rubinstein et al.   Cell Host & Microbe

Antibiotic resistance—the need for global solutions

(2013) Ramanan Laxminarayan et al.   LANCET INFECTIOUS DISEASES

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Insights into type 1 diabetes provided by genetic analyses

(2013) Grant Morahan   Current Opinion in Endocrinology Diabetes and Obesity

Bacteriophages as Pathogens and Immune Modulators?

(2013) A. Lengeling et al.   mBio

Stability and Infectivity of Cytolethal Distending Toxin Type V Gene-Carrying Bacteriophages in a Water Mesocosm and under Different Inactivation Conditions

(2012) Anna Allué-Guardia et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) A. Stern et al.   GENOME RESEARCH

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Host-Gut Microbiota Metabolic Interactions

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

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

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

A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

(2012) Gilda Grard et al.   PLoS Pathogens

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Archaea as emerging organisms in complex human microbiomes

(2011) Bédis Dridi et al.   ANAEROBE

Reversing Bacterial Resistance to Antibiotics by Phage-Mediated Delivery of Dominant Sensitive Genes

(2011) Rotem Edgar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2011) S. Minot et al.   GENOME RESEARCH

The cell biology of receptor-mediated virus entry

(2011) Joe Grove et al.   JOURNAL OF CELL BIOLOGY

Gut Microbiome Metagenomics Analysis Suggests a Functional Model for the Development of Autoimmunity for Type 1 Diabetes

(2011) Christopher T. Brown et al.   PLoS One

Successful Transmission of a Retrovirus Depends on the Commensal Microbiota

(2011) M. Kane et al.   SCIENCE

Metagenomic Analysis of the Viral Communities in Fermented Foods

(2010) Eun-Jin Park et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine

(2010) Ken Cadwell et al.   CELL

Phage Therapy in Clinical Practice: Treatment of Human Infections

(2010) Elizabeth Kutter et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults

(2010) Nadja Larsen et al.   PLoS One

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistantPseudomonas aeruginosa; a preliminary report of efficacy

(2009) A. Wright et al.   CLINICAL OTOLARYNGOLOGY

Current insights into phage biodiversity and biogeography

(2009) Rebecca Vega Thurber   CURRENT OPINION IN MICROBIOLOGY

Shiga Toxin as a Bacterial Defense against a Eukaryotic Predator, Tetrahymena thermophila

(2009) W. Lainhart et al.   JOURNAL OF BACTERIOLOGY

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

Viral Trigger for Type 1 Diabetes: Pros and Cons

(2008) C. M. Filippi et al.   DIABETES