Fishing for phages in metagenomes: what do we catch, what do we miss?

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes

(2021) Katelyn McNair et al.   Microorganisms

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter

(2021) Moïra B Dion et al.   NUCLEIC ACIDS RESEARCH

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

(2021) Natalya Yutin et al.   Nature Communications

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

(2021) Martial Marbouty et al.   eLife

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

(2021) Jiarong Guo et al.   Microbiome

Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR

(2021) Eric G. Sakowski et al.   Nature Microbiology

Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review

(2021) Julie Callanan et al.   Microorganisms

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

(2020) John Beaulaurier et al.   GENOME RESEARCH

Global Organization and Proposed Megataxonomy of the Virus World

(2020) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome

(2020) Eugene V. Koonin et al.   TRENDS IN MICROBIOLOGY

Discovery of several thousand highly diverse circular DNA viruses

(2020) Michael J Tisza et al.   eLife

Resurrection of a global, metagenomically defined Gokushovirus

(2020) Paul C Kirchberger et al.   eLife

Expansion of known ssRNA phage genomes: From tens to over a thousand

(2020) J. Callanan et al.   Science Advances

The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

(2020)   Nature Microbiology

Metaviral SPAdes: assembly of viruses from metagenomic data

(2020) Dmitry Antipov et al.   BIOINFORMATICS

Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation

(2020) Alfred Fillol-Salom et al.   CURRENT OPINION IN MICROBIOLOGY

Structure and mechanism of DNA delivery of a gene transfer agent

(2020) Pavol Bárdy et al.   Nature Communications

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

(2020) Kristopher Kieft et al.   Microbiome

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

(2020) Yuri I. Wolf et al.   Nature Microbiology

Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes

(2020) Sergey A. Shmakov et al.   Communications Biology

Seeker: alignment-free identification of bacteriophage genomes by deep learning

(2020) Noam Auslander et al.   NUCLEIC ACIDS RESEARCH

Structure and function of virion RNA polymerase of a crAss-like phage

(2020) Arina V. Drobysheva et al.   NATURE

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Rapid de novo evolution of lysis genes in single-stranded RNA phages

(2020) Karthik R. Chamakura et al.   Nature Communications

Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

(2020) Manuel Kleiner et al.   Microbiome

The Missing Tailed Phages: Prediction of Small Capsid Candidates

(2020) Antoni Luque et al.   Microorganisms

CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans

(2019) César Díez-Villaseñor et al.   Nature Communications

Megaphages infect Prevotella and variants are widespread in gut microbiomes

(2019) Audra E. Devoto et al.   Nature Microbiology

Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis

(2019) Lasha Gogokhia et al.   Cell Host & Microbe

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins

(2019) J. Leonardo Moreno-Gallego et al.   Cell Host & Microbe

PHANOTATE: a novel approach to gene identification in phage genomes

(2019) Katelyn McNair et al.   BIOINFORMATICS

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

(2019) Simon Roux et al.   Nature Microbiology

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

(2019) Robert A. Edwards et al.   Nature Microbiology

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog

(2019) Paola Soto-Perez et al.   Cell Host & Microbe

Genomic comparison of 60 completely sequenced bacteriophages that infect Erwinia and/or Pantoea bacteria

(2019) Daniel W. Thompson et al.   VIROLOGY

The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None

(2019) Chandrabali Ghose et al.   Frontiers in Microbiology

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

(2019) Evan P. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural puzzles in virology solved with an overarching icosahedral design principle

(2019) Reidun Twarock et al.   Nature Communications

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

(2019) Eitan Yaffe et al.   Nature Microbiology

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe

(2018) Alfred Fillol-Salom et al.   ISME Journal

Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis

(2018) Natalya Yutin et al.   Virology Journal

Anti-phage islands force their target phage to directly mediate island excision and spread

(2018) Amelia C. McKitterick et al.   Nature Communications

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

(2018) Kathryn M. Kauffman et al.   NATURE

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

Origins and Evolution of the Global RNA Virome

(2018) Yuri I. Wolf et al.   mBio

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

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

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

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Hyperexpansion of RNA Bacteriophage Diversity

(2016) Siddharth R. Krishnamurthy et al.   PLOS BIOLOGY

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

(2016) Branko Rihtman et al.   PeerJ

Viruses as Winners in the Game of Life

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

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

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

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Stop codon reassignments in the wild

(2014) N. N. Ivanova et al.   SCIENCE

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Optimal architectures of elongated viruses

(2010) A. Luque et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE