ArticlemSystems2022
Deciphering Active Prophages from Metagenomes.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
52 citing papers in PubMed, 67 citations in OpenAlex.
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
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- Beyond Bacteria: The Emerging Role of the Gut Virome and Mycobiome in Celiac Disease.Nutrients · 2026Review
- Chemical prophage induction selectively removes Vibrio from a pelagic Sargassum-derived multispecies biofilm.Environmental microbiome · 2026Article
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- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- The effects of bacteriophage cocktail treatment on healthy gut microbiota: anMicrobial genomics · 2026Article
- V- and VNature communications · 2026Article
- The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.mSystems · 2026Article
- Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.Nature communications · 2026Article
- Distinct prokaryotic gut microbiome and proviral-immune axes of pathophysiology in Sickle Cell Disease.bioRxiv : the preprint server for biology · 2026Article
- Species-specific prophage induction by ciprofloxacin in human gut metagenomes.bioRxiv : the preprint server for biology · 2026Article
- Metagenomics reveals potential interactions between Patescibacteriota and their phages in groundwater ecosystems.mSystems · 2026Article
- Integrated meta-omics reveals AFBMicrobiome · 2025Article
- Article
- Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.Nature microbiology · 2025Article
- Prophage Activation: An In Silico Platform for Identifying Prophage Regulatory Elements to Inform Phage Engineering Against Drug-Resistant Bacteria.Life (Basel, Switzerland) · 2025Article
- Deeper Exploration of Gut Microbiome: Profile of Resistome, Virome and Viral Auxiliary Metabolic Genes of Three Ethnic Indian Groups.Molecular biotechnology · 2025Article
- Interactions and evolutionary relationships among bacterial mobile genetic elements.Nature reviews. Microbiology · 2025Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Temperate phages (prophages) are ubiquitous in nature and persist as dormant components of host cells (lysogenic stage) before activating and lysing the host (lytic stage). Actively replicating prophages contribute to central community processes, such as enabling bacterial virulence, manipulating biogeochemical cycling, and driving microbial community diversification. Recent advances in sequencing technology have allowed for the identification and characterization of diverse phages, yet no approaches currently exist for identifying if a prophage has activated. Here, we present PropagAtE (Prophage Activity Estimator), an automated software tool for estimating if a prophage is in the lytic or lysogenic stage of infection. PropagAtE uses statistical analyses of prophage-to-host read coverage ratios to decipher actively replicating prophages, irrespective of whether prophages were induced or spontaneously activated. We demonstrate that PropagAtE is fast, accurate, and sensitive, regardless of sequencing depth. Application of PropagAtE to prophages from 348 complex metagenomes from human gut, murine gut, and soil environments identified distinct spatial and temporal prophage activation signatures, with the highest proportion of active prophages in murine gut samples. In infants treated with antibiotics or infants without treatment, we identified active prophage populations correlated with specific treatment groups. Within time series samples from the human gut, 11 prophage populations, some encoding the sulfur metabolism gene
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.