ArticleScience advances2017
Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.
Article in Science advances, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 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
76 citing papers in PubMed.
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.Journal of water and health · 2026Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.PLoS biology · 2025Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.bioRxiv : the preprint server for biology · 2025Article
- A roadmap to understanding and anticipating microbial gene transfer in soil communities.Microbiology and molecular biology reviews : MMBR · 2025Review
- From resistance to remedy: the role of clustered regularly interspaced short palindromic repeats system in combating antimicrobial resistance-a review.Naunyn-Schmiedeberg's archives of pharmacology · 2025Review
- The chromatin landscape of the histone-possessingGenome research · 2025Article
- Review
- Detection of rare plasmid hosts using a targeted Hi-C approach.ISME communications · 2025Article
- A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.Microbiome · 2024Article
- Dietary Effects on the Gut Phageome.International journal of molecular sciences · 2024Review
- Establishing Host-Virus Link Through Host Metabolism: Viral DNA SIP Validation Using T4 Bacteriophage and E. coli.Current microbiology · 2024Article
- Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle.Scientific reports · 2024Article
- Orchestrating chromosome conformation capture analysis with Bioconductor.Nature communications · 2024Article
- Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages.Nature communications · 2024Article
- The Diversity of Bacteriophages in the Human Gut.Methods in molecular biology (Clifton, N.J.) · 2024Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The biochemical activities of microbial communities, or microbiomes, are essential parts of environmental and animal ecosystems. The dynamics, balance, and effects of these communities are strongly influenced by phages present in the population. Being able to characterize bacterium-phage relationships is therefore essential to investigate these ecosystems to the full extent of their complexity. However, this task is currently limited by (i) the ability to characterize complete bacterial and viral genomes from a complex mix of species and (ii) the difficulty to assign phage sequences to their bacterial hosts. We show that both limitations can be circumvented using meta3C, an experimental and computational approach that exploits the physical contacts between DNA molecules to infer their proximity. In a single experiment, dozens of bacterial and phage genomes present in a complex mouse gut microbiota were assembled and scaffolded de novo. The phage genomes were then assigned to their putative bacterial hosts according to the physical contacts between the different DNA molecules, opening new perspectives for a comprehensive picture of the genomic structure of the gut flora. Therefore, this work holds far-reaching implications for human health studies aiming to bridge the virome to the microbiome.
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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.