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

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

(2019) Gareth Trubl et al.   PeerJ

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

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

(2017) Anja Narr et al.   Frontiers in Microbiology

Contribution of cropland to the spread of Shiga toxin phages and the emergence of new Shiga toxin-producing strains

(2017) Pablo Quirós et al.   Scientific Reports

Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes

(2016) Jéssica Subirats et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

(2016) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

(2016) Gareth Trubl et al.   PeerJ

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

(2015) Brian Reavy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and Ecology of Viruses in Hyperarid Desert Soils

(2015) Olivier Zablocki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis

(2015) Nádia Conceição-Neto et al.   Scientific Reports

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

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils

(2014) Olivier Zablocki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metagenomic analysis of the viral community in Namib Desert hypoliths

(2014) Evelien M. Adriaenssens et al.   ENVIRONMENTAL MICROBIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Lesley Hoyles et al.   RESEARCH IN MICROBIOLOGY

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The flows of nitrogen, bacteria and viruses from the soil to water compartments are influenced by earthworm activity and organic fertilization (compost vs. vermicompost)

(2013) Joël Amossé et al.   SOIL BIOLOGY & BIOCHEMISTRY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

T4-Related Bacteriophage LIMEstone Isolates for the Control of Soft Rot on Potato Caused by ‘Dickeya solani’

(2012) Evelien M. Adriaenssens et al.   PLoS One

Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

(2012) L. Deng et al.   mBio

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

Viruses in soils: morphological diversity and abundance in the rhizosphere

(2009) M.M. Swanson et al.   ANNALS OF APPLIED BIOLOGY

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH