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The landscape of lysogeny across microbial community density, diversity and energetics

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Observations on the relationship of symbiotic and lytic bacteriophage

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Bacterioplankton in the coastal euphotic zone: Distribution, activity and possible relationships with phytoplankton

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Lysogenization by bacteriophage lambda

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The effect of temperature and algal biomass on bacterial production and specific growth rate in freshwater and marine habitats

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The Occurrence of Lysogenic Bacteria and Microbial Aggregates in the Lakes of the McMurdo Dry Valleys, Antarctica

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A Single-Cell Analysis of Virioplankton Adsorption, Infection, and Intracellular Abundance in Different Bacterioplankton Physiologic Categories

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Viral dynamics and patterns of lysogeny in saline Antarctic lakes

inferredcites →https://doi.org/10.1007/s00338-010-0612-7openalex-snapshot

Organic matter release by dominant hermatypic corals of the Northern Red Sea

inferredcites →https://doi.org/10.1007/s12275-014-4083-3openalex-snapshot

When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness

inferredcites →https://doi.org/10.1016/j.bpj.2017.09.012openalex-snapshot

Late-Arriving Signals Contribute Less to Cell-Fate Decisions

inferredcites →https://doi.org/10.1016/j.cell.2012.06.036openalex-snapshot

Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence

inferredcites →https://doi.org/10.1016/j.cell.2019.03.040openalex-snapshot

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

inferredcites →https://doi.org/10.1016/j.chom.2019.01.017openalex-snapshot

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

inferredcites →https://doi.org/10.1016/j.chom.2020.01.004openalex-snapshot

Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner

inferredcites →https://doi.org/10.1016/j.coviro.2019.05.013openalex-snapshot

What is (not) known about the dynamics of the human gut virome in health and disease

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Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense

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Standing stocks, production, and respiration of phytoplankton and heterotrophic bacteria in the western Arctic Ocean

inferredcites →https://doi.org/10.1016/j.mib.2017.04.010openalex-snapshot

Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer

inferredcites →https://doi.org/10.1016/j.scib.2020.12.014openalex-snapshot

Revisiting marine lytic and lysogenic virus-host interactions: Kill-the-Winner and Piggyback-the-Winner

inferredcites →https://doi.org/10.1016/j.soilbio.2013.07.007openalex-snapshot

The flows of nitrogen, bacteria and viruses from the soil to water compartments are influenced by earthworm activity and organic fertilization (compost vs. vermicompost)

inferredcites →https://doi.org/10.1016/j.soilbio.2020.107767openalex-snapshot

Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity

inferredcites →https://doi.org/10.1016/j.tim.2016.02.008openalex-snapshot

Why Be Temperate: Lessons from Bacteriophage λ

inferredcites →https://doi.org/10.1016/j.tim.2017.12.004openalex-snapshot

The ‘Neglected’ Soil Virome – Potential Role and Impact

inferredcites →https://doi.org/10.1016/j.watres.2004.03.008openalex-snapshot

Rapid enumeration of virus-like particles in drinking water samples using SYBR green I-staining

inferredcites →https://doi.org/10.1016/s0300-9084(75)80274-4openalex-snapshot

Lysogenization by bacteriophage lambda

inferredcites →https://doi.org/10.1038/ismej.2008.35openalex-snapshot

Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?

inferredcites →https://doi.org/10.1038/ismej.2010.181openalex-snapshot

Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons

inferredcites →https://doi.org/10.1038/ismej.2012.161openalex-snapshot

Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages

inferredcites →https://doi.org/10.1038/ismej.2015.125openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ismej.2015.48openalex-snapshot

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton

inferredcites →https://doi.org/10.1038/ismej.2016.47openalex-snapshot

Genetic and life-history traits associated with the distribution of prophages in bacteria

inferredcites →https://doi.org/10.1038/ismej.2016.51openalex-snapshot

Temperate phages enhance pathogen fitness in chronic lung infection

inferredcites →https://doi.org/10.1038/ismej.2016.79openalex-snapshot

Prophages mediate defense against phage infection through diverse mechanisms

inferredcites →https://doi.org/10.1038/ismej.2016.90openalex-snapshot

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

inferredcites →https://doi.org/10.1038/ismej.2017.190openalex-snapshot

Phage mobility is a core determinant of phage–bacteria coexistence in biofilms

inferredcites →https://doi.org/10.1038/nature09199openalex-snapshot

Viruses in the faecal microbiota of monozygotic twins and their mothers

inferredcites →https://doi.org/10.1038/nature11921openalex-snapshot

Abundant SAR11 viruses in the ocean

inferredcites →https://doi.org/10.1038/nature17193openalex-snapshot

Lytic to temperate switching of viral communities

inferredcites →https://doi.org/10.1038/nature21049openalex-snapshot

Communication between viruses guides lysis–lysogeny decisions

inferredcites →https://doi.org/10.1038/nature23296openalex-snapshot

Knowles & Rohwer reply

inferredcites →https://doi.org/10.1038/ncomms1146openalex-snapshot

Cryptic prophages help bacteria cope with adverse environments

inferredcites →https://doi.org/10.1038/ncomms13333openalex-snapshot

Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells

inferredcites →https://doi.org/10.1038/ncomms14341openalex-snapshot

Cell fate decisions emerge as phages cooperate or compete inside their host

inferredcites →https://doi.org/10.1038/ncomms15955openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nmicrobiol.2015.24openalex-snapshot

Re-examination of the relationship between marine virus and microbial cell abundances

inferredcites →https://doi.org/10.1038/nmicrobiol.2016.251openalex-snapshot

Prophage-mediated defence against viral attack and viral counter-defence

inferredcites →https://doi.org/10.1038/nmicrobiol.2016.42openalex-snapshot

Global microbialization of coral reefs

inferredcites →https://doi.org/10.1038/nmicrobiol.2017.64openalex-snapshot

Variability and host density independence in inductions-based estimates of environmental lysogeny

inferredcites →https://doi.org/10.1038/npjbiofilms.2016.10openalex-snapshot

Piggyback-the-Winner in host-associated microbial communities

inferredcites →https://doi.org/10.1038/s41396-018-0061-9openalex-snapshot

Lysogeny is prevalent and widely distributed in the murine gut microbiota

inferredcites →https://doi.org/10.1038/s41396-020-00795-9openalex-snapshot

Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms

inferredcites →https://doi.org/10.1038/s41396-020-00870-1openalex-snapshot

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

inferredcites →https://doi.org/10.1038/s41396-020-0604-8openalex-snapshot

Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

inferredcites →https://doi.org/10.1038/s41396-020-0637-zopenalex-snapshot

Genetically similar temperate phages form coalitions with their shared host that lead to niche-specific fitness effects

inferredcites →https://doi.org/10.1038/s41396-020-0641-3openalex-snapshot

High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum

inferredcites →https://doi.org/10.1038/s41467-020-18078-4openalex-snapshot

Temperate infection in a virus–host system previously known for virulent dynamics

inferredcites →https://doi.org/10.1038/s41467-020-18164-7openalex-snapshot

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

inferredcites →https://doi.org/10.1038/s41467-021-23698-5openalex-snapshot

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

inferredcites →https://doi.org/10.1038/s41559-017-0424-zopenalex-snapshot

Phage–host population dynamics promotes prophage acquisition in bacteria with innate immunity

inferredcites →https://doi.org/10.1038/s41559-018-0568-5openalex-snapshot

A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function

inferredcites →https://doi.org/10.1038/s41564-018-0259-7openalex-snapshot

Structural and functional insights into the regulation of the lysis–lysogeny decision in viral communities

inferredcites →https://doi.org/10.1038/s41564-019-0526-2openalex-snapshot

Defining the human gut host–phage network through single-cell viral tagging

inferredcites →https://doi.org/10.1038/s41564-019-0625-0openalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41564-020-0725-xopenalex-snapshot

Lysogenic host–virus interactions in SAR11 marine bacteria

inferredcites →https://doi.org/10.1038/s41579-020-00444-0openalex-snapshot

Single-virus genomics and beyond

inferredcites →https://doi.org/10.1038/s41586-019-1453-3openalex-snapshot

Cholera toxin promotes pathogen acquisition of host-derived nutrients

inferredcites →https://doi.org/10.1038/s41598-019-52794-2openalex-snapshot

Impact of bacteria motility in the encounter rates with bacteriophage in mucus

inferredcites →https://doi.org/10.1038/s41598-020-61417-0openalex-snapshot

Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount

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Proteolysis of the phage λ CII regulatory protein by FtsH (HflB) of Escherichia coli

inferredcites →https://doi.org/10.1046/j.1365-2958.2003.03580.xopenalex-snapshot

Prophages and bacterial genomics: what have we learned so far?

inferredcites →https://doi.org/10.1073/pnas.1300833110openalex-snapshot

Rapid evolution of the human gut virome

inferredcites →https://doi.org/10.1073/pnas.1305923110openalex-snapshot

Bacteriophage adhering to mucus provide a non–host-derived immunity

inferredcites →https://doi.org/10.1073/pnas.1521291113openalex-snapshot

Scaling laws predict global microbial diversity

inferredcites →https://doi.org/10.1073/pnas.69.2.366openalex-snapshot

Establishment of Repression by Lambdoid Phage in Catabolite Activator Protein and Adenylate Cyclase Mutants of Escherichia coli

inferredcites →https://doi.org/10.1073/pnas.75.11.5594openalex-snapshot

Analysis of bacteriophage P1 immunity by using lambda-P1 recombinants constructed in vitro.

inferredcites →https://doi.org/10.1073/pnas.85.21.7882openalex-snapshot

Cleavage of the cII protein of phage lambda by purified HflA protease: control of the switch between lysis and lysogeny.

inferredcites →https://doi.org/10.1093/bioinformatics/bts014openalex-snapshot

PHACTS, a computational approach to classifying the lifestyle of phages

inferredcites →https://doi.org/10.1093/femsre/fuv048openalex-snapshot

Computational approaches to predict bacteriophage–host relationships

inferredcites →https://doi.org/10.1093/molbev/mss279openalex-snapshot

The Adaptation of Temperate Bacteriophages to Their Host Genomes

inferredcites →https://doi.org/10.1093/nar/gkl732openalex-snapshot

Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences

inferredcites →https://doi.org/10.1093/ve/vex011openalex-snapshot

Viral coinfection is shaped by host ecology and virus–virus interactions across diverse microbial taxa and environments

inferredcites →https://doi.org/10.1098/rspb.2016.0467openalex-snapshot

Energetic differences between bacterioplankton trophic groups and coral reef resistance

inferredcites →https://doi.org/10.1099/00221287-21-3-676openalex-snapshot

Conditions for the Infection of Escherichia coli with Lambda Phage and for the Establishment of Lysogeny

inferredcites →https://doi.org/10.1099/00221287-23-3-457openalex-snapshot

The Growth of Micro-organisms in Relation to their Energy Supply

inferredcites →https://doi.org/10.1101/2020.03.13.990044openalex-snapshot

FITNESS BENEFITS TO BACTERIA OF CARRYING PROPHAGES AND PROPHAGE-ENCODED ANTIBIOTIC-RESISTANCE GENES PEAK IN DIFFERENT ENVIRONMENTS

inferredcites →https://doi.org/10.1101/2020.03.18.996918openalex-snapshot

Population dynamics of decision making in temperate bacteriophages

inferredcites →https://doi.org/10.1101/2020.04.08.028340openalex-snapshot

Phage and bacteria diversification through a prophage acquisition ratchet

inferredcites →https://doi.org/10.1101/824235openalex-snapshot

The population and evolutionary dynamics of bacteriophage: Why be temperate revisited

inferredcites →https://doi.org/10.1101/gad.8.10.1212openalex-snapshot

Specificity determinants for the interaction of lambda repressor and P22 repressor dimers.

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The human gut virome: Inter-individual variation and dynamic response to diet

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Coevolution Maintains Diversity in the Stochastic “Kill the Winner” Model

inferredcites →https://doi.org/10.1111/1462-2920.12120openalex-snapshot

Linking the lytic and lysogenic bacteriophage cycles to environmental conditions, host physiology and their variability in coastal lagoons

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Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound: D evil's H ole, B ermuda

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Microbial and sponge loops modify fish production in phase‐shifting coral reefs

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Pelagiphages in the Podoviridae family integrate into host genomes

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

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Benchmarking of s ingle‐virus genomics: a new tool for uncovering the virosphere

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Deciphering the virus‐to‐prokaryote ratio ( VPR ): insights into virus–host relationships in a variety of ecosystems

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Fitness benefits to bacteria of carrying prophages and prophage‐encoded antibiotic‐resistance genes peak in different environments

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Virus and microbial loop dynamics over an annual cycle in three contrasting Antarctic lakes

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Bacteria between protists and phages: from antipredation strategies to the evolution of pathogenicity

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Incidence of lysogeny within temperate and extreme soil environments

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Viral‐mediated lysis of microbes and carbon release in the sub‐Antarctic and Polar Frontal zones of the Australian Southern Ocean

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Seasonal variations of phage life strategies and bacterial physiological states in three northern temperate lakes

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Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

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Unveiling the role and life strategies of viruses from the surface to the dark ocean

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Virus-Bacterium Interactions in Water and Sediment of West African Inland Aquatic Systems

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Prevalence of Lysogeny among Soil Bacteria and Presence of 16S rRNA and trzN Genes in Viral-Community DNA

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Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

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Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean

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Lysogenization of Escherichia coli him+, himA, and himD hosts by bacteriophage Mu

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THE ESTABLISHMENT OF LYSOGENICITY IN ESCHERICHIA COLI

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Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

inferredcites →https://doi.org/10.1128/mbio.00805-16openalex-snapshot

Genomes of Abundant and Widespread Viruses from the Deep Ocean

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Evolution of Superinfection Immunity in Cluster A Mycobacteriophages

inferredcites →https://doi.org/10.1128/mbio.01903-17openalex-snapshot

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior

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Evolutionary Ecology of Prokaryotic Immune Mechanisms

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Energetics of bacterial growth: balance of anabolic and catabolic reactions

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Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion

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Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

inferredcites →https://doi.org/10.1128/msystems.00084-22openalex-snapshot

Deciphering Active Prophages from Metagenomes

inferredcites →https://doi.org/10.1128/msystems.00353-20openalex-snapshot

Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles

inferredcites →https://doi.org/10.1128/msystems.00554-19openalex-snapshot

Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean

inferredcites →https://doi.org/10.1146/annurev-marine-122414-033938openalex-snapshot

Growth Rates of Microbes in the Oceans

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Single-Cell Studies of Phage λ: Hidden Treasures Under Occam's Rug

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THE LYSIS-LYSOGENY DECISION OF PHAGE λ: EXPLICIT PROGRAMMING AND RESPONSIVENESS

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Switches in Bacteriophage Lambda Development

inferredcites →https://doi.org/10.1186/s12864-020-6523-2openalex-snapshot

Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes

inferredcites →https://doi.org/10.1186/s12866-018-1229-1openalex-snapshot

Spontaneously induced prophages are abundant in a naturally evolved bacterial starter culture and deliver competitive advantage to the host

inferredcites →https://doi.org/10.1186/s40168-020-00867-0openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pone.0027973openalex-snapshot

Effects of Coral Reef Benthic Primary Producers on Dissolved Organic Carbon and Microbial Activity

inferredcites →https://doi.org/10.1371/journal.pone.0043233openalex-snapshot

Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score

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Bacterial and viral dynamics during a mass coral spawning period on the Great Barrier Reef

inferredcites →https://doi.org/10.3354/ame01262openalex-snapshot

Distribution of heterotrophic bacteria and virus-like particles along a salinity gradient in a hypersaline coastal lagoon

inferredcites →https://doi.org/10.3354/meps08653openalex-snapshot

Organic matter release by Red Sea coral reef organisms—potential effects on microbial activity and in situ O2 availability

inferredcites →https://doi.org/10.3354/meps104163openalex-snapshot

Seasonal and diel abundance of viruses and occurrence of lysogeny/bacteriocinogeny in the marine environment

inferredcites →https://doi.org/10.3354/meps142027openalex-snapshot

Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction

inferredcites →https://doi.org/10.3389/fmicb.2014.00264openalex-snapshot

Fracture zones in the Mid Atlantic Ridge lead to alterations in prokaryotic and viral parameters in deep-water masses

inferredcites →https://doi.org/10.3389/fmicb.2014.00493openalex-snapshot

Unprecedented evidence for high viral abundance and lytic activity in coral reef waters of the South Pacific Ocean

inferredcites →https://doi.org/10.3389/fmicb.2015.00615openalex-snapshot

The complex relationship between microbial growth rate and yield and its implications for ecosystem processes

inferredcites →https://doi.org/10.3389/fmicb.2017.01386openalex-snapshot

In silico Evolution of Lysis-Lysogeny Strategies Reproduces Observed Lysogeny Propensities in Temperate Bacteriophages

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Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters

inferredcites →https://doi.org/10.3390/microorganisms9061115openalex-snapshot

Prophage Genomics and Ecology in the Family Rhodobacteraceae

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Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host–Viral Relationships in an Arctic Marine Ecosystem

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Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems

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Virus‐like particle distribution and abundance in sediments and overlying waters along eutrophication gradients in two subtropical estuaries

inferredcites →https://doi.org/10.4319/lo.2004.49.2.0459openalex-snapshot

Virus production and life strategies in aquatic sediments

inferredcites →https://doi.org/10.4319/lo.2004.49.6.2073openalex-snapshot

Virus and bacteria dynamics of a coastal sediment: Implication for benthic carbon cycling

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Detection of lysogeny in marine environments

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Response of ocean phytoplankton community structure to climate change over the 21st century: partitioning the effects of nutrients, temperature and light

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Biophysical and physiological processes causing oxygen loss from coral reefs

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Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Viral Abundance and Lysogenic Fraction are Affected More by Sampling Date than Long-Term Conservation Land Management Practices

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PSOSP uncovers pervasive SOS‐independent prophages with distinct genomic and host traits in bacterial genomes

inferred← citeshttps://doi.org/10.1007/978-1-0716-3549-0_15openalex-snapshot

Bacteriophage–Host Interactions and Coevolution

inferred← citeshttps://doi.org/10.1007/978-1-0716-3549-0_3openalex-snapshot

Breaking the Ice: A Review of Phages in Polar Ecosystems

inferred← citeshttps://doi.org/10.1007/978-3-031-76692-3_10openalex-snapshot

Ecosystem Microbiology of Coral Reefs

inferred← citeshttps://doi.org/10.1007/978-3-031-76692-3_11openalex-snapshot

Coral Reef Microbialization and Viralization Shape Ecosystem Health, Stability, and Resilience

inferred← citeshttps://doi.org/10.1007/s00248-022-02167-6openalex-snapshot

Significant Differences in Planktonic Virus Communities Between “Cellular Fraction” (0.22 ~ 3.0 µm) and “Viral Fraction” (< 0.22 μm) in the Ocean

inferred← citeshttps://doi.org/10.1007/s00284-026-04801-9openalex-snapshot

The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance

inferred← citeshttps://doi.org/10.1007/s00374-023-01765-xopenalex-snapshot

Extraction optimisation to measure viral abundance in red soils

inferred← citeshttps://doi.org/10.1007/s10532-025-10181-xopenalex-snapshot

Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk

inferred← citeshttps://doi.org/10.1016/bs.aambs.2025.08.002openalex-snapshot

Heads or tails? An insight into the nature of antibacterial proteins of entomopathogenic bacteria

inferred← citeshttps://doi.org/10.1016/j.agee.2024.109078openalex-snapshot

Viral abundance and lysogenic fraction respond dynamically to cover-crop burn down and vary with conservation soil management practices

inferred← citeshttps://doi.org/10.1016/j.ages.2025.100002openalex-snapshot

Trojan phages: Distinguishing lysogeny from transduction in phage-involved ARG dissemination

inferred← citeshttps://doi.org/10.1016/j.apsoil.2025.106436openalex-snapshot

Mitomycin C-induced prophage activation for exploring the Lysogeny-lysis functional dynamics in situ

inferred← citeshttps://doi.org/10.1016/j.cej.2025.161877openalex-snapshot

Plasticizers determine a deeper reshape of soil virome than microplastics

inferred← citeshttps://doi.org/10.1016/j.celrep.2026.117491openalex-snapshot

Prophage induction contributes to alterations in the gut phageome during intestinal inflammation

inferred← citeshttps://doi.org/10.1016/j.chom.2022.04.006openalex-snapshot

The pediatric virome in health and disease

inferred← citeshttps://doi.org/10.1016/j.chom.2026.07.001openalex-snapshot

Unveiling active microbial processes in Earth’s deepest seawater

inferred← citeshttps://doi.org/10.1016/j.csbj.2021.12.032openalex-snapshot

Predicting the capsid architecture of phages from metagenomic data

inferred← citeshttps://doi.org/10.1016/j.cub.2024.05.032openalex-snapshot

Coinfecting phages impede each other’s entry into the cell

inferred← citeshttps://doi.org/10.1016/j.ecochg.2022.100057openalex-snapshot

Marine cyanobacteria in the anthropocene: Are top-down paradigms robust to climate change?

inferred← citeshttps://doi.org/10.1016/j.hal.2023.102409openalex-snapshot

Sequencing the genomes of LPP-1, the first isolated cyanophage, and its relative LPP-2 reveal different integration mechanisms in closely related phages

inferred← citeshttps://doi.org/10.1016/j.isci.2023.106007openalex-snapshot

Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota

inferred← citeshttps://doi.org/10.1016/j.mib.2022.102245openalex-snapshot

Functional ecology of bacteriophages in the environment

inferred← citeshttps://doi.org/10.1016/j.phage.2026.100006openalex-snapshot

Viruses infecting microbial hosts: Biological interactions and therapeutic, biocontrol, and environmental applications bacteriophages: Microbial parasites unleashed for pioneering applications

inferred← citeshttps://doi.org/10.1016/j.scitotenv.2023.164465openalex-snapshot

Machine learning sheds light on physical-chemical and biological parameters leading to Abrolhos coral reef microbialization

inferred← citeshttps://doi.org/10.1016/j.tim.2022.11.009openalex-snapshot

Unique relationships between phages and endospore-forming hosts

inferred← citeshttps://doi.org/10.1016/j.watres.2025.124270openalex-snapshot

Prevalence and functional impact of the interactions between lysogenic phages and hosts in activated sludge systems: Insights from large-scale metagenomics and experimental evidence

inferred← citeshttps://doi.org/10.1016/j.watres.2026.126466openalex-snapshot

Viral suppression constrains environmentally stimulated microbial methylmercury production in wastewater treatment plants

inferred← citeshttps://doi.org/10.1021/acs.est.6c02641openalex-snapshot

Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes

inferred← citeshttps://doi.org/10.1038/s41467-023-44157-3openalex-snapshot

Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication

inferred← citeshttps://doi.org/10.1038/s41467-024-51913-6openalex-snapshot

Using bacterial population dynamics to count phages and their lysogens

inferred← citeshttps://doi.org/10.1038/s41467-024-51946-xopenalex-snapshot

Stable coexistence between an archaeal virus and the dominant methanogen of the human gut

inferred← citeshttps://doi.org/10.1038/s41467-024-53317-yopenalex-snapshot

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape

inferred← citeshttps://doi.org/10.1038/s41467-025-66733-5openalex-snapshot

Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis

inferred← citeshttps://doi.org/10.1038/s41467-026-76431-5openalex-snapshot

Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau

inferred← citeshttps://doi.org/10.1038/s41522-026-00939-3openalex-snapshot

The epidermal ecotone: a proposed model system for marine viral ecology at the animal-environmental interface

inferred← citeshttps://doi.org/10.1038/s42003-026-10106-1openalex-snapshot

Phage bioaugmentation reveals the potential of lysogeny for soil bioremediation

inferred← citeshttps://doi.org/10.1042/ebc20250035openalex-snapshot

The role of phages in plant-associated microbial communities

inferred← citeshttps://doi.org/10.1073/pnas.2115145119openalex-snapshot

Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo's paradox

inferred← citeshttps://doi.org/10.1073/pnas.2419798121openalex-snapshot

Adaptive expression of phage auxiliary metabolic genes in paddy soils and their contribution toward global carbon sequestration

inferred← citeshttps://doi.org/10.1093/femsle/fnac091openalex-snapshot

Viral life strategies in a heavily anthropized tropical lagoon

inferred← citeshttps://doi.org/10.1093/gbe/evag079openalex-snapshot

On the Low Abundance of Antibiotic Resistance Genes in Bacteriophage Genomes and Their Random Acquisition via Specialized Transduction

inferred← citeshttps://doi.org/10.1093/ismeco/ycae084openalex-snapshot

Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool

inferred← citeshttps://doi.org/10.1093/ismeco/ycae143openalex-snapshot

Viral diversity and host associations in microbial electrolysis cells

inferred← citeshttps://doi.org/10.1093/ismejo/wrae240openalex-snapshot

Host-specific viral predation network on coral reefs

inferred← citeshttps://doi.org/10.1093/ismejo/wraf110openalex-snapshot

Viralization as a microbial approach for enhancing coral reef restoration

inferred← citeshttps://doi.org/10.1093/ismejo/wrag197openalex-snapshot

Abundance–activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes

inferred← citeshttps://doi.org/10.1093/molbev/msaf259openalex-snapshot

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage

inferred← citeshttps://doi.org/10.1093/ve/veae028openalex-snapshot

Lytic/Lysogenic Transition as a Life-History Switch

inferred← citeshttps://doi.org/10.1098/rspb.2023.1531openalex-snapshot

Drivers of microbial food-web structure along productivity gradients

inferred← citeshttps://doi.org/10.1099/mgen.0.001166openalex-snapshot

Prophages: an integral but understudied component of the human microbiome

inferred← citeshttps://doi.org/10.1101/2022.01.26.477855openalex-snapshot

Phage Paride hijacks bacterial stress responses to kill dormant, antibiotic-tolerant cells

inferred← citeshttps://doi.org/10.1101/2022.12.09.519740openalex-snapshot

Ecological and evolutionary patterns of virus-host interactions throughout a grassland soil depth profile

inferred← citeshttps://doi.org/10.1101/2023.04.17.536465openalex-snapshot

A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria

inferred← citeshttps://doi.org/10.1101/2023.04.20.537752openalex-snapshot

The Promise and Pitfalls of Prophages

inferred← citeshttps://doi.org/10.1101/2023.05.04.539508openalex-snapshot

Prophage rates in the human microbiome vary by body site and host health

inferred← citeshttps://doi.org/10.1101/2023.12.27.573307openalex-snapshot

Emergence of tipping points and transient dynamics in finite observations

inferred← citeshttps://doi.org/10.1101/2024.03.13.584929openalex-snapshot

Soil viruses reduce greenhouse gas emissions and promote microbial necromass accrual

inferred← citeshttps://doi.org/10.1101/2024.04.02.587543openalex-snapshot

The low abundance of antimicrobial resistance genes (ARGs) in bacteriophages and their transfer bottlenecks limit the ability of phages to contribute to the spread of ARGs

inferred← citeshttps://doi.org/10.1111/1462-2920.16457openalex-snapshot

Top‐heavy trophic structure within benthic viral dark matter

inferred← citeshttps://doi.org/10.1111/1462-2920.70155openalex-snapshot

Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont

inferred← citeshttps://doi.org/10.1111/1462-2920.70204openalex-snapshot

Omnipresent Allies: The Role of Temperate Phages in Microbial Adaptation Across Ecosystems

inferred← citeshttps://doi.org/10.1111/gcb.17524openalex-snapshot

Estimating the Importance of Viral Contributions to Soil Carbon Dynamics

inferred← citeshttps://doi.org/10.1111/gcb.70412openalex-snapshot

Viral Diversity Mediates Carbon Allocation for Ecosystem Multifunctionality Across Biomes

inferred← citeshttps://doi.org/10.1126/science.ado0713openalex-snapshot

A phage tail–like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria

inferred← citeshttps://doi.org/10.1128/jb.00458-25openalex-snapshot

From hijackers to architects: the role of prophages in bacterial genome evolution

inferred← citeshttps://doi.org/10.1128/jvi.01420-23openalex-snapshot

The phage fought the cells, and the phage won: a satellite symposium at the ASV 2023 annual meeting

inferred← citeshttps://doi.org/10.1128/mbio.01569-22openalex-snapshot

Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column

inferred← citeshttps://doi.org/10.1128/mbio.02246-23openalex-snapshot

Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile

inferred← citeshttps://doi.org/10.1128/mmbr.00086-23openalex-snapshot

The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy

inferred← citeshttps://doi.org/10.1128/mmbr.00254-25openalex-snapshot

To lyse or not to lyse: biasing bacteriophage behaviors

inferred← citeshttps://doi.org/10.1128/msystems.00083-24openalex-snapshot

Snow viruses and their implications on red snow algal blooms

inferred← citeshttps://doi.org/10.1128/msystems.00395-26openalex-snapshot

Bacteriophage replication strategies are associated with organic matter energy content on coral reefs

inferred← citeshttps://doi.org/10.1128/msystems.00807-22openalex-snapshot

What Lies Beneath? Taking the Plunge into the Murky Waters of Phage Biology

inferred← citeshttps://doi.org/10.1128/msystems.01364-24openalex-snapshot

Improving gut virome comparisons using predicted phage host information

inferred← citeshttps://doi.org/10.1186/s12866-026-05031-6openalex-snapshot

Genomic and experimental characterization of unique Antarctic temperate phage Perkons reveals multiple integrases and complex lysogenic dynamics in Psychrobacillus sp. L4

inferred← citeshttps://doi.org/10.1186/s12915-023-01571-9openalex-snapshot

Viral predation pressure on coral reefs

inferred← citeshttps://doi.org/10.1186/s13059-024-03236-4openalex-snapshot

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

inferred← citeshttps://doi.org/10.1186/s40168-023-01666-zopenalex-snapshot

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

inferred← citeshttps://doi.org/10.1186/s40168-025-02085-yopenalex-snapshot

Viral activity in lake analogs of anoxic early Earth oceans

inferred← citeshttps://doi.org/10.1186/s40168-025-02173-zopenalex-snapshot

Global biogeography of airborne viruses in public transit systems and their host interactions

inferred← citeshttps://doi.org/10.1186/s40168-026-02362-4openalex-snapshot

Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction

inferred← citeshttps://doi.org/10.1371/journal.pbio.3003063openalex-snapshot

Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage–host interactions

inferred← citeshttps://doi.org/10.1371/journal.pone.0296038openalex-snapshot

Bacteriophage-encoded 24B_1 molecule resembles herpesviral microRNAs and plays a crucial role in the development of both the virus and its host

inferred← citeshttps://doi.org/10.21203/rs.3.rs-1931579/v1openalex-snapshot

Disinfectant Stress Enhances Prokaryotic Symbiosis with Lysogenic Phages and Defense Systems Against Detrimental Phage Infection

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3356289/v1openalex-snapshot

Large-scale genome-centric metagenomics reveals the prevalence of lysogenic virus-host interactions in activated sludge

inferred← citeshttps://doi.org/10.21203/rs.3.rs-9607317/v1openalex-snapshot

Molecular Characterization and In Vitro Lytic Activity of LysLm680, an Endolysin Derived from Temperate Listeria Phages

inferred← citeshttps://doi.org/10.2139/ssrn.4969383openalex-snapshot

A Symbiogenic Origin for Prokaryotes

inferred← citeshttps://doi.org/10.2166/wst.2026.332openalex-snapshot

Uncovering a hidden diversity of aquatic bacteriophages: ecological diversity, untapped therapeutic potential, and water quality control

inferred← citeshttps://doi.org/10.22541/au.166618890.06191324/v1openalex-snapshot

A diverse community of bacteriophage may contribute to insect prey degradation in pitcher plants

inferred← citeshttps://doi.org/10.3389/fnut.2025.1694264openalex-snapshot

Intestinal dysbiosis associated with non-nutritive sweeteners intake: an effect without a cause?

inferred← citeshttps://doi.org/10.3390/microorganisms10081671openalex-snapshot

How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research

inferred← citeshttps://doi.org/10.3390/microorganisms13112474openalex-snapshot

Heterotrophic Prokaryote Host–Virus Dynamics During Spring in the Northeast Atlantic Ocean

inferred← citeshttps://doi.org/10.3390/microorganisms13112503openalex-snapshot

Prospects of Phage DJ6712 and FW6709 in Biocontrol of Aeromonas veronii in Fish Aquaculture

inferred← citeshttps://doi.org/10.3390/v15020420openalex-snapshot

When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages

inferred← citeshttps://doi.org/10.3390/v16111750openalex-snapshot

Soybean Bradyrhizobium spp. Spontaneously Produce Abundant and Diverse Temperate Phages in Culture

inferred← citeshttps://doi.org/10.3390/v18080814openalex-snapshot

Evolutionarily Optimal Phage Life-History Traits: Burst Size vs. Lysis Time

inferred← citeshttps://doi.org/10.48130/aee-0026-0003openalex-snapshot

Soil microplastics hidden web: interaction of microbes and viruses as a frontier for sustainable ecosystem recovery

inferred← citeshttps://doi.org/10.6084/m9.figshare.22625239openalex-snapshot

Additional file 2 of Viral predation pressure on coral reefs

inferred← citeshttps://doi.org/10.6084/m9.figshare.24452529openalex-snapshot

Additional file 1 of Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

inferred← citeshttps://doi.org/10.6084/m9.figshare.24452589openalex-snapshot

Additional file 2 of Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

inferred← citeshttps://doi.org/10.6084/m9.figshare.25608690openalex-snapshot

Additional file 1 of Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

inferred← citeshttps://doi.org/10.6084/m9.figshare.25608862openalex-snapshot

Additional file 2 of Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

inferred← citeshttps://doi.org/10.6084/m9.figshare.26707020openalex-snapshot

Additional file 3 of Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes

inferred← citeshttps://doi.org/10.64898/2025.12.02.691978openalex-snapshot

Secret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms

inferred← citeshttps://doi.org/10.64898/2026.07.21.739416openalex-snapshot

Implicit representation of viruses fails to capture impacts of virus-induced mortality in global marine ecosystem models

inferred← citeshttps://doi.org/10.70675/291d4522zca29z4156z936ezdcea44fc811bopenalex-snapshot

Caractérisation du virome d’un écosystème tropical fortement anthropisé : la lagune Ebrié en Côte d’Ivoire

inferred← citeshttps://doi.org/10.70675/d473c943z420fz449cza66ezcd8c0b5257d0openalex-snapshot

Experimental evolution of the wine-associated bacterium Oenococcus oeni in extreme environments : application to the selection of improved malolactic starters

inferred← citeshttps://doi.org/10.71246/cuca3026openalex-snapshot

REVISITING: Genomic Analysis of Uncultured Marine Viral Communities

inferred← citeshttps://doi.org/10.7554/elife.103107openalex-snapshot

Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation with implications for gut colonization dynamics in Ciona robusta

inferred← citeshttps://doi.org/10.7554/elife.103107.1openalex-snapshot

Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation: implications for gut colonization dynamics in Ciona robusta

inferred← citeshttps://doi.org/10.7554/elife.103107.2openalex-snapshot

Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation: implications for gut colonization dynamics in Ciona robusta

inferred← citeshttps://doi.org/10.7554/elife.103107.3openalex-snapshot

Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation with implications for gut colonization dynamics in Ciona robusta

inferred← citeshttps://doi.org/10.7717/peerj.12194openalex-snapshot

Phage strategies facilitate bacterial coexistence under environmental variability

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