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2024
Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome
Microorganisms
2024
Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment
Environment International
2024
The gut virome is associated with stress-induced changes in behaviour and immune responses in mice
Nature Microbiology
2024
The infant gut virome is associated with preschool asthma risk independently of bacteria
Nature Medicine
2024
Metagenomic evaluation of the performance of passive Moore swabs for sewage monitoring relative to composite sampling over time resolved deployments
Water Research
2024
Evidence of Zika Virus Reinfection by Genome Diversity and Antibody Response Analysis, Brazil
Emerging Infectious Diseases
2024
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies
Microbial Genomics
2024
Soil Microbiology, Ecology and Biochemistry
2024
A metagenomic catalog of the early-life human gut virome
Nature Communications
2024
Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations
ISME Communications
2024
Efficient Recovery of Complete Gut Viral Genomes by Combined Short‐ and Long‐Read Sequencing
Advanced Science
2023
Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA
Viruses
2023
Computational Biology
2023
Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance.
Environmental Research
2023
Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data
Microbiome
2023
Benchmarking State-of-the-Art Approaches for Norovirus Genome Assembly in Metagenome Sample
Biology
2023
Bioinformatic approaches for studying the microbiome of fermented food
Critical Reviews in Microbiology
2023
High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community
mSystems
2023
MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets
ISME Communications
2023
ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis
Gut Microbes
2023
Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota
iScience
2023
Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils
Nature Ecology & Evolution
2023
Enhanced Viral Metagenomics with Lazypipe 2
Viruses
2023
Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability
Microbiome
2023
Marine viruses disperse bidirectionally along the natural water cycle
Nature Communications
2023
Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community
Journal of Virology
2023
Virome reveals effect of Ulva prolifera green tide on the structural and functional profiles of virus communities in coastal environments
Science of The Total Environment
2023
Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in “Pink Berry” Marine Microbial Aggregates
Applied and Environmental Microbiology
2023
Significant Differences in Planktonic Virus Communities Between “Cellular Fraction” (0.22 ~ 3.0 µm) and “Viral Fraction” (< 0.22 μm) in the Ocean
Microbial Ecology
2023
Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines
Microbiome
2023
Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile
mBio
2023
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Bioinformatics
2023
Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes
The ISME Journal
2023
Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety
Nature Communications
2023
Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles
Nature Communications
2023
Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick
ISME Communications
2023
Revisiting evolutionary trajectories and the organization of the Pleolipoviridae family
PLOS Genetics
2022
Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus
Proceedings of the National Academy of Sciences
2022
Exploring Virome Diversity in Public Data in South America as an Approach for Detecting Viral Sources From Potentially Emerging Viruses
Frontiers in Genetics
2022
Bacteriophages Roam the Wheat Phyllosphere
Viruses
2022
Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2
OMICS: A Journal of Integrative Biology
2022
A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary
Scientific Data
2022
Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica
Applied and Environmental Microbiology
2022
VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data
Frontiers in Bioinformatics
2022
A Novel Alteromonas Phage Lineage with a Broad Host Range and Small Burst Size
Microbiology Spectrum
2022
Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis
Microbiome
2022
Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management
Viruses
2022
Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth
The ISME Journal
2022
Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
Science
2022
MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations
Microbiome
2022
vRhyme enables binning of viral genomes from metagenomes
Nucleic Acids Research
2022
Distribution of rare N4‐like viruses in temperate estuaries unveiled by viromics
Environmental Microbiology
2022
Diversity and Ecology of Caudoviricetes Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts
Viruses
2022
Droplet Microfluidics for High-Resolution Virology
Analytical Chemistry
2022
Virus genomics: what is being overlooked?
Current Opinion in Virology
2022
PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets
Life
2022
Diversity in the soil virosphere: to infinity and beyond?
Trends in Microbiology
2022
Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients
Viruses
2022
Uncovering 1058 Novel Human Enteric DNA Viruses Through Deep Long-Read Third-Generation Sequencing and Their Clinical Impact
Gastroenterology
2022
Spaceflight Virology: What Do We Know about Viral Threats in the Spaceflight Environment?
Astrobiology
2022
Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere
Microbiome
2022
Uncovering novel human gut virome using ultra-deep metagenomic sequencing
Chinese Medical Journal
2022
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages
The ISME Journal
2022
A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria
Applied and Environmental Microbiology
2022
RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels
ISME Communications
2022
Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean
The ISME Journal
2022
Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts
Cell Reports
2022
A comparative study of flow cytometry‐sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant
iMeta
2021
Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats
Microbiology Spectrum
2021
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters
The ISME Journal
2021
A new family of “megaphages” abundant in the marine environment
ISME Communications
2021
Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities
mSystems
2021
Probing the Mobilome: Discoveries in the Dynamic Microbiome
Trends in Microbiology
2021
Encyclopedia of Virology
2021
Encyclopedia of Virology
2021
Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads
DNA Research
2021
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
Nature Microbiology
2021
Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil
mSystems
2021
Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale
mSystems
2021
Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria
The ISME Journal
2021
Stability of the human gut virome and effect of gluten-free diet
Cell Reports
2021
mMGE: a database for human metagenomic extrachromosomal mobile genetic elements
Nucleic Acids Research
2021
Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms
Frontiers in Microbiology
2021
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation
PeerJ
2021
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses
Briefings in Bioinformatics
2021
Fishing for phages in metagenomes: what do we catch, what do we miss?
Current Opinion in Virology
2021
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Nature Biotechnology
2021
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
Microbiome
2021
Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations
Microbiome
2021
Integrating Viral Metagenomics into an Ecological Framework
Annual Review of Virology
2021
Glacier ice archives nearly 15,000-year-old microbes and phages
Microbiome
2021
Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome
iScience
2021
VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature
PeerJ
2021
Dynamics of Baltic Sea phages driven by environmental changes
Environmental Microbiology
2021
Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential
Cell Host & Microbe
2021
LABRADOR—A Computational Workflow for Virus Detection in High-Throughput Sequencing Data
Viruses
2021
Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation
Gastroenterology
2021
The gut virome in Irritable Bowel Syndrome differs from that of controls
Gut Microbes
2021
The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome
Frontiers in Cellular and Infection Microbiology
2021
Perspective on taxonomic classification of uncultivated viruses
Current Opinion in Virology
2021
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog
mSystems
2021
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
Microbiome
2021
Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut
Viruses
2021
Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities
The ISME Journal
2020
Virome assembly and annotation in brain tissue based on next‐generation sequencing
Cancer Medicine
2020
Diverse and unique viruses discovered in the surface water of the East China Sea
BMC Genomics
2020
Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples
PLOS ONE
2020
Emerging technologies for the rapid detection of enteric viruses in the aquatic environment
Current Opinion in Environmental Science & Health
2020
Single-virus genomics and beyond
Nature Reviews Microbiology
2020
Metaviral SPAdes: assembly of viruses from metagenomic data
Bioinformatics
2020
Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota
Proceedings of the National Academy of Sciences
2020
Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline
The ISME Journal
2020
Shining Light on Human Gut Bacteriophages
Frontiers in Cellular and Infection Microbiology
2020
Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
Genome Research
2020
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts
Cell Host & Microbe
2020
Diversity and Host Interactions among Virulent and Temperate Baltic Sea Flavobacterium Phages
Viruses
2020
Coral Bleaching Phenotypes Associated With Differential Abundances of Nucleocytoplasmic Large DNA Viruses
Frontiers in Marine Science
2020
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
Cell Host & Microbe
2020
Bacteriophage of the Skin Microbiome in Patients with Psoriasis and Healthy Family Controls
Journal of Investigative Dermatology
2020
Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics
Soil Systems
2020
Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model
Gut
2020
Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column
The ISME Journal
2020
Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice
mSystems
2019
Riding the wave of genomics to investigate aquatic coliphage diversity and activity
Environmental Microbiology
2019
Gut Bacteriophage: Current Understanding and Challenges
Frontiers in Endocrinology
2019
Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins
Cell Host & Microbe
2019
Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean
The ISME Journal
2019
Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease
Cell Host & Microbe
2019
Metagenomic Approaches for Detecting Viral Diversity in Water Environments
Journal of Environmental Engineering
2019
A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”
mSystems
2019
The Battle Within: Interactions of Bacteriophages and Bacteria in the Gastrointestinal Tract
Cell Host & Microbe
2019
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
Cell
2019
A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion
Cell Host & Microbe
2019
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
PeerJ
2019
The Landscape of Genetic Content in the Gut and Oral Human Microbiome
Cell Host & Microbe
2019
Mini‐Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences
Advanced Biosystems
2019
Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems
The ISME Journal
2019
Host-hijacking and planktonic piracy: how phages command the microbial high seas
Virology Journal
2019
Next-generation sequencing of dsRNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO
Microbial Genomics
2019
Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses
Frontiers in Microbiology
2019
Benchmarking protocols for the metagenomic analysis of stream biofilm viromes
PeerJ
2019
Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet
Viruses
2019
Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341
Applied and Environmental Microbiology
2019
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
PeerJ
2019
Minimum Information about an Uncultivated Virus Genome (MIUViG)
Nature Biotechnology
2019
Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications
2019
Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake
Environmental Microbiology
2019
Choice of assembly software has a critical impact on virome characterisation
Microbiome
2018
The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages
Marine Genomics
2018
Deciphering the Human Virome with Single-Virus Genomics and Metagenomics
Viruses
2018
Notes on recombination and reassortment in multipartite/segmented viruses
Current Opinion in Virology
2018
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
PeerJ
2018
Viral Communities of Shark Bay Modern Stromatolites
Frontiers in Microbiology
2018
Methods in Molecular Biology
2018
Nanopore-based detection and characterization of yam viruses
Scientific Reports
2018
Methods in Molecular Biology
2018
Murine colitis reveals a disease-associated bacteriophage community
Nature Microbiology
2018
MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
Frontiers in Genetics
2018
Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions
Viruses
2018
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing
mSystems
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