Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes

(2022) Xiaoxuan Zheng et al.   ISME Journal

Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench

(2022) Jiulong Zhao et al.   mSystems

Marine biofilms: diversity, interactions and biofouling

(2022) Pei-Yuan Qian et al.   NATURE REVIEWS MICROBIOLOGY

vRhyme enables binning of viral genomes from metagenomes

(2022) Kristopher Kieft et al.   NUCLEIC ACIDS RESEARCH

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

(2021) Zexin Li et al.   ISME Journal

Causes and Consequences of Bacteriophage Diversification via Genetic Exchanges across Lifestyles and Bacterial Taxa

(2021) Jorge A Moura de Sousa et al.   MOLECULAR BIOLOGY AND EVOLUTION

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

(2021) Jiarong Guo et al.   Microbiome

Diversity and distribution of viruses inhabiting the deepest ocean on Earth

(2021) Huahua Jian et al.   ISME Journal

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

(2021) Ryan Cook et al.   Microbiome

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses

(2021) Bradley W. Wright et al.   mSystems

Virus-associated organosulfur metabolism in human and environmental systems

(2021) Kristopher Kieft et al.   Cell Reports

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

(2021) Akbar Adjie Pratama et al.   PeerJ

Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress

(2021) Dan Huang et al.   Microbiome

Biogeographical distributions of nitrogen‐cycling functional genes in a subtropical estuary

(2021) Pandeng Wang et al.   FUNCTIONAL ECOLOGY

Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

(2021) Sophie K. Jurgensen et al.   ISME Journal

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

(2021) Anneliek M. ter Horst et al.   Microbiome

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

Phage diversity, genomics and phylogeny

(2020) Moïra B. Dion et al.   NATURE REVIEWS MICROBIOLOGY

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

(2020) Asier Zaragoza-Solas et al.   mSystems

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

(2020) Kira Moon et al.   Microbiome

Differences in metabolic potential between particle-associated and free-living bacteria along Pearl River Estuary

(2020) Yanyang Liu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

(2020) Shao-Ming Gao et al.   Microbiome

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

(2020) Kristopher Kieft et al.   Microbiome

Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

(2020) Matthew J. Tuttle et al.   ENVIRONMENTAL MICROBIOLOGY

Sensing of O 2 and nitrate by bacteria: Alternative strategies for transcriptional regulation of nitrate respiration by O 2 and nitrate

(2020) Gottfried Unden et al.   ENVIRONMENTAL MICROBIOLOGY

Large freshwater phages with the potential to augment aerobic methane oxidation

(2020) Lin-Xing Chen et al.   Nature Microbiology

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

(2020) M. Consuelo Gazitúa et al.   ISME Journal

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig

(2020) Saisai Zhou et al.   Frontiers in Microbiology

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

(2020) F. H. Coutinho et al.   Microbiome

The communities and functional profiles of virioplankton along a salinity gradient in a subtropical estuary

(2020) Chen Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Compositional changes of sedimentary microbes in the Yangtze River Estuary and their roles in the biochemical cycle

(2020) Lili Liu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Host-hijacking and planktonic piracy: how phages command the microbial high seas

(2019) Joanna Warwick-Dugdale et al.   Virology Journal

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

(2019) Amy E. Zimmerman et al.   NATURE REVIEWS MICROBIOLOGY

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

The insertion of the non-heme Fe B cofactor into nitric oxide reductase from P . denitrificans depends on NorQ and NorD accessory proteins

(2018) Maximilian Kahle et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Discordance Between Resident and Active Bacterioplankton in Free-Living and Particle-Associated Communities in Estuary Ecosystem

(2018) Jia-Ling Li et al.   MICROBIAL ECOLOGY

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

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

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

(2018) Paula Dalcin Martins et al.   Microbiome

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

(2018) Nathan A. Ahlgren et al.   ISME Journal

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

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

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

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

(2017) Tianliang He et al.   mBio

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

(2017) Felipe H. Coutinho et al.   Nature Communications

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

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

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

The Significance of Mutualistic Phages for Bacterial Ecology and Evolution

(2016) Nancy Obeng et al.   TRENDS IN MICROBIOLOGY

Virocell Metabolism: Metabolic Innovations During Host–Virus Interactions in the Ocean

(2016) Shilo Rosenwasser et al.   TRENDS IN MICROBIOLOGY

The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses

(2016) Lisa T. Crummett et al.   VIROLOGY

Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China

(2016) Xinzhen Wang et al.   Scientific Reports

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

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics

(2015) Jennifer R Brum et al.   ISME Journal

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

(2013) Nana Yaw D Ankrah et al.   ISME Journal

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

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

(2012) Limin Fu et al.   BIOINFORMATICS

Marine Viruses Exploit Their Host's Two-Component Regulatory System in Response to Resource Limitation

(2012) Qinglu Zeng et al.   CURRENT BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Iron monosulfide enrichment and the presence of organosulfur in eutrophic estuarine sediments

(2011) Bree Morgan et al.   CHEMICAL GEOLOGY

HMMER web server: interactive sequence similarity searching

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Viruses manipulate the marine environment

(2009) Forest Rohwer et al.   NATURE