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

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

The human urine virome in association with urinary tract infections

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

Conservation of streptococcal CRISPRs on human skin and saliva

(2014) Refugio Robles-Sikisaka et al.   BMC MICROBIOLOGY

Characterization of bacteriophage communities and CRISPR profiles from dental plaque

(2014) Mayuri Naidu et al.   BMC MICROBIOLOGY

Phage and bacteria support mutual diversity in a narrowing staircase of coexistence

(2014) Jan O Haerter et al.   ISME Journal

Human oral viruses are personal, persistent and gender-consistent

(2014) Shira R Abeles et al.   ISME Journal

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

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

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy

(2013) Iwijn De Vlaminck et al.   CELL

Association between living environment and human oral viral ecology

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

Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

(2013) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

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

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

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform

(2012) Andrew S. Whiteley et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

(2012) Vincent Foulongne 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

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

(2011) S. Minot et al.   GENOME RESEARCH

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

Antibiotics in Feed Induce Prophages in Swine Fecal Microbiomes

(2011) H. K. Allen et al.   mBio

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

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

Collateral Effects of Antibiotics: Carbadox and Metronidazole Induce VSH-1 and Facilitate Gene Transfer among Brachyspira hyodysenteriae Strains

(2008) T. B. Stanton 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

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH