Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome

(2020) Lance Boling et al.   Gut Microbes

Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts

(2020) Kosuke Fujimoto et al.   Cell Host & Microbe

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization

(2020) Tao Zuo et al.   Cell Host & Microbe

Dietary Fructose and Microbiota-Derived Short-Chain Fatty Acids Promote Bacteriophage Production in the Gut Symbiont Lactobacillus reuteri

(2019) Jee-Hwan Oh et al.   Cell Host & Microbe

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins

(2019) J. Leonardo Moreno-Gallego et al.   Cell Host & Microbe

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

Lysogeny is prevalent and widely distributed in the murine gut microbiota

(2018) Min-Soo Kim et al.   ISME Journal

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier 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

Chemical transformation of xenobiotics by the human gut microbiota

(2017) Nitzan Koppel et al.   SCIENCE

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Variability and host density independence in inductions-based estimates of environmental lysogeny

(2017) Ben Knowles et al.   Nature Microbiology

The influence of non-steroidal anti-inflammatory drugs on the gut microbiome

(2016) M.A.M. Rogers et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

Prophages mediate defense against phage infection through diverse mechanisms

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

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

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

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Chemotherapy-driven dysbiosis in the intestinal microbiome

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

Trends in Prescription Drug Use Among Adults in the United States From 1999-2012

(2015) Elizabeth D. Kantor et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Local bacteria affect the efficacy of chemotherapeutic drugs

(2015) Panos Lehouritis et al.   Scientific Reports

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG

(2014) Jonathan Crabtree et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Short-Term Effect of Antibiotics on Human Gut Microbiota

(2014) Suchita Panda et al.   PLoS One

A perspective on the epidemiology of acetaminophen exposure and toxicity in the United States

(2014) Marissa Blieden et al.   Expert Review of Clinical Pharmacology

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Differential Effects of Antibiotic Therapy on the Structure and Function of Human Gut Microbiota

(2013) Ana Elena Pérez-Cobas et al.   PLoS One

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Techniques used to characterize the gut microbiota: a guide for the clinician

(2012) Marianne H. Fraher et al.   Nature Reviews Gastroenterology & Hepatology

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

Fake virus particles generated by fluorescence microscopy

(2012) Patrick Forterre et al.   TRENDS IN MICROBIOLOGY

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

(2011) S. Minot et al.   GENOME RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

Comparative Analyses of Prophage-Like Elements Present in Bifidobacterial Genomes

(2009) M. Ventura et al.   APPLIED AND ENVIRONMENTAL 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