Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants

Distribution of soil viruses across China and their potential role in phosphorous metabolism

(2022) Li-Li Han et al.   Environmental Microbiome

A mixed blessing of viruses in wastewater treatment plants

(2022) Ling-Dong Shi et al.   WATER RESEARCH

Genomes of six viruses that infect Asgard archaea from deep-sea sediments

(2022) Ian M. Rambo et al.   Nature Microbiology

Roadmap for Managing SARS-CoV-2 and other Viruses in the Water Environment for Public Health

(2021) Gang Liu et al.   Engineering

Pathogenic and Indigenous Denitrifying Bacteria are Transcriptionally Active and Key Multi-Antibiotic-Resistant Players in Wastewater Treatment Plants

(2021) Ling Yuan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants

(2021) Yiqiang Chen et al.   Nature Communications

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

(2021) Kristopher Kieft et al.   Nature Communications

Virus-associated organosulfur metabolism in human and environmental systems

(2021) Kristopher Kieft et al.   Cell Reports

Prophage Genomics and Ecology in the Family Rhodobacteraceae

(2021) Kathryn Forcone et al.   Microorganisms

Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages

(2020) Aurélie Mathieu et al.   Nature Communications

Recent Advances in Metabolic Pathways of Sulfate Reduction in Intestinal Bacteria

(2020) Ivan Kushkevych et al.   Cells

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

(2020) Paraskevi Mara et al.   ISME Journal

Large freshwater phages with the potential to augment aerobic methane oxidation

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

Genome‐resolved viral ecology in a marine oxygen minimum zone

(2020) Dean Vik et al.   ENVIRONMENTAL 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

Survey of the bacteriophage phoH gene in wetland sediments in northeast China

(2019) Xiang Li et al.   Scientific Reports

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

(2019) Ella T. Sieradzki et al.   Nature Communications

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Global diversity and biogeography of bacterial communities in wastewater treatment plants

(2019) Linwei Wu et al.   Nature Microbiology

Sulfur metabolites in the pelagic ocean

(2019) Mary Ann Moran et al.   NATURE REVIEWS MICROBIOLOGY

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

The ‘Neglected’ Soil Virome – Potential Role and Impact

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

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

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

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

Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes

(2018) Feng Ju et al.   ISME Journal

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

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

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Sulfide production and oxidation by heterotrophic bacteria under aerobic conditions

(2017) Yongzhen Xia et al.   ISME Journal

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

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

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

(2017) Benjamin Bolduc et al.   PeerJ

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks

(2017) Ramzan Kh. Umarov et al.   PLoS One

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

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Viral infection of the marine alga Emiliania huxleyi triggers lipidome remodeling and induces the production of highly saturated triacylglycerol

(2016) Sergey Malitsky et al.   NEW PHYTOLOGIST

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

(2016) Shilo Rosenwasser et al.   TRENDS IN MICROBIOLOGY

phoDAlkaline Phosphatase Gene Diversity in Soil

(2015) Sabine A. Ragot et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

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

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

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages

(2015) Simon Roux et al.   Frontiers in Microbiology

Deep sequencing of the viralphoHgene reveals temporal variation, depth-specific composition, and persistent dominance of the same viralphoHgenes in the Sargasso Sea

(2015) Dawn B. Goldsmith et al.   PeerJ

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Bonnie L Hurwitz et al.   ISME Journal

Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant

(2014) Feng Ju et al.   ISME Journal

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis

(2014) Hagay Enav et al.   Microbiome

Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants

(2013) Feng Ju et al.   ENVIRONMENTAL MICROBIOLOGY

Abundant SAR11 viruses in the ocean

(2013) Yanlin Zhao et al.   NATURE

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

Twelve previously unknown phage genera are ubiquitous in global oceans

(2013) K. Holmfeldt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs

(2012) Basma El Yacoubi et al.   Annual Review of Genetics

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

(2012) Qinglu Zeng et al.   CURRENT BIOLOGY

The virocell concept and environmental microbiology

(2012) Patrick Forterre   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge

(2012) Ke Yu et al.   PLoS One

Development ofphoHas a Novel Signature Gene for Assessing Marine Phage Diversity

(2011) Dawn B. Goldsmith et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate

(2011) Hideyuki Tamaki et al.   ENVIRONMENTAL 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

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism

(2011) L. R. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current understanding of fatty acid biosynthesis and the acyl carrier protein

(2010) David I. Chan et al.   BIOCHEMICAL JOURNAL

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

Global regulation by the seven-component Pi signaling system

(2010) Yi-Ju Hsieh et al.   CURRENT OPINION IN MICROBIOLOGY

Chemical composition of organic matters in domestic wastewater

(2010) Man-hong Huang et al.   DESALINATION

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

(2010) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

Genome Annotation and Intraviral Interactome for the Streptococcus pneumoniae Virulent Phage Dp-1

(2010) M. Sabri et al.   JOURNAL OF BACTERIOLOGY

Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur

(2010) Martha H. Stipanuk et al.   JOURNAL OF INHERITED METABOLIC DISEASE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Major viral impact on the functioning of benthic deep-sea ecosystems

(2008) Roberto Danovaro et al.   NATURE