ArticleeLife2021
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety.Nature communications · 2023Trial
- Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome.bioRxiv : the preprint server for biology · 2026Article
- Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.Environmental microbiology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding.Nature communications · 2026Article
- Segmented filamentous bacteria are worldwide human gut commensals.Nature communications · 2026Article
- Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.Environmental science and ecotechnology · 2026Article
- 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
- Article
- MVPHI: a multi-view learning framework for predicting complex microbial interactions.Scientific reports · 2025Article
- 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
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
- Article
- Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.bioRxiv : the preprint server for biology · 2025Article
- Viral activity in lake analogs of anoxic early Earth oceans.Microbiome · 2025Article
- Gut phages and their interactions with bacterial and mammalian hosts.Journal of bacteriology · 2025Review
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics, and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarters of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.
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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.