Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

(2021) Christian Santos-Medellin et al.   ISME Journal

Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil

(2020) Pauline C. Göller et al.   Microbiome

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils

(2020) Li Bi et al.   ENVIRONMENTAL MICROBIOLOGY

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

(2020) Kira Moon et al.   Microbiome

A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer

(2020) Sankalp Arya et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2020) Kristopher Kieft et al.   Microbiome

Evaluation of Potential ARG Packaging by Two Environmental T7-Like Phage during Phage-Host Interaction

(2020) Junlin Liu et al.   Viruses-Basel

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Soil Viruses: A New Hope

(2019) Joanne B. Emerson   mSystems

Viruses as key reservoirs of antibiotic resistance genes in the environment

(2019) Didier Debroas et al.   ISME Journal

The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated blaCTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial Pathogens

(2019) Ekaterine Gabashvili et al.   CURRENT MICROBIOLOGY

Infectious phage particles packaging antibiotic resistance genes found in meat products and chicken feces

(2019) Clara Gómez-Gómez et al.   Scientific Reports

Exploring the profile of antimicrobial resistance genes harboring by bacteriophage in chicken feces

(2019) Yanxian Yang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Targeted inactivation of antibiotic-resistant Escherichia coli and Pseudomonas aeruginosa in a soil-lettuce system by combined polyvalent bacteriophage and biochar treatment

(2018) Mao Ye et al.   ENVIRONMENTAL POLLUTION

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

Exploring Viral Diversity in a Unique South African Soil Habitat

(2018) Jane Segobola et al.   Scientific Reports

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems

(2018) Yulin Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Antibiotic resistance genes in bacteriophages from diverse marine habitats

(2018) William Calero-Cáceres et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Exploring the contribution of bacteriophages to antibiotic resistance

(2017) Itziar Lekunberri et al.   ENVIRONMENTAL POLLUTION

Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands

(2017) Xiao-Bo Wang et al.   ISME Journal

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils

(2017) Li-Li Han et al.   Scientific Reports

Detecting Lactococcus lactis Prophages by Mitomycin C-Mediated Induction Coupled to Flow Cytometry Analysis

(2017) Joana Oliveira et al.   Frontiers in Microbiology

Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

(2017) Stefano Colombo et al.   Frontiers in Microbiology

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

Environmental drivers of viral community composition in Antarctic soils identified by viromics

(2017) Evelien M. Adriaenssens et al.   Microbiome

ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database

(2016) Ying Yang et al.   BIOINFORMATICS

Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil

(2016) Qinglin Chen et al.   ENVIRONMENT INTERNATIONAL

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistence of naturally occurring antibiotic resistance genes in the bacteria and bacteriophage fractions of wastewater

(2016) William Calero-Cáceres et al.   WATER RESEARCH

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes

(2015) Amira Shousha et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread

(2014) Victoriya V. Volkova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Sludge As a Potential Important Source of Antibiotic Resistance Genes in Both the Bacterial and Bacteriophage Fractions

(2014) William Calero-Cáceres et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Effect of different long-term fertilization regimes on the viral community in an agricultural soil of Southern China

(2014) Lin Chen et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Environment

(2014) Jose Luis Balcazar   PLoS Pathogens

Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Human Fecal Samples

(2013) Pablo Quirós et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Identification of Viral Pathogen Diversity in Sewage Sludge by Metagenome Analysis

(2013) Kyle Bibby et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2013) Sheetal R. Modi et al.   NATURE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses

(2011) Kyoung-Ho Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota

(2011) L. Fancello et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Ecology of viruses in soils: Past, present and future perspectives

(2010) Makoto Kimura et al.   SOIL SCIENCE AND PLANT NUTRITION

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

Virus adsorption and inactivation in soil as influenced by autochthonous microorganisms and water content

(2007) Bingzi Zhao et al.   SOIL BIOLOGY & BIOCHEMISTRY