Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus-host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage-host signals. Sequence homology approaches are the most effective at identifying known phage-host pairs. Compositional and abundance-based methods contain significant signal for phage-host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current know...Continue Reading
Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. III. Failure of superinfecting phage DNA to enter sieA+ lysogens
Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. IV. Genetics and physiology of sieB exclusion
Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. 1. Exclusion of generalized transducing particles
Prevalence of broad-host-range lytic bacteriophages of Sphaerotilus natans, Escherichia coli, and Pseudomonas aeruginosa
Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies
Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria.
Characterization of the integrase gene and attachment site for the Myxococcus xanthus bacteriophage Mx9.
A broad-host-range, generalized transducing phage (SN-T) acquires 16S rRNA genes from different genera of bacteria
Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time
Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage
Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
Contrasting life strategies of viruses that infect photo- and heterotrophic bacteria, as revealed by viral tagging
Development of a high throughput assay for indirectly measuring phage growth using the OmniLog(TM) system
Short-term observations of marine bacterial and viral communities: patterns, connections and resilience
Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
Safety analysis of a Russian phage cocktail: from metagenomic analysis to oral application in healthy human subjects
Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists
Coevolutionary diversification creates nested-modular structure in phage-bacteria interaction networks
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Bacteria-phage interactions across time and space: merging local adaptation and time-shift experiments to understand phage evolution
Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics
Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes
The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay
Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome
Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges
A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments
Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341
Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake
An Uncultivated Virus Infecting a Nanoarchaeal Parasite in the Hot Springs of Yellowstone National Park
The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition.
Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples
Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles
Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean
In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes
CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans
Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes.
Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia
A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples
Computational prediction of inter-species relationships through omics data analysis and machine learning
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
Approaches to optimize therapeutic bacteriophage and bacteriophage-derived products to combat bacterial infections
Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities.
Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism
Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences
Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential
Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses.
The communities and functional profiles of virioplankton along a salinity gradient in a subtropical estuary
Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics.
A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.
Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge.
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.
Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system.
Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history.
Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses.
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities.
Bacteriophage: Phage Therapy
Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.