ArticleScience advances2024
Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.
Article in Science advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction.Scientific reports · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.Cancer biology & medicine · 2026Review
- Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.Microbiome · 2026Article
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- Grand challenge in microbiome data science: recovering the microbiome as a system.Frontiers in microbiology · 2026Article
- Article
- Genomic landscape of completeFrontiers in microbiology · 2026Article
- Maternal consumption of urbanized diet compromises early-life health in association with gut microbiota.Gut microbes · 2025Review
- Genetic exchange networks bridge mobile DNA vehicles in the bacterial pathogen Listeria monocytogenes.Nature communications · 2025Article
- The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.Environmental microbiome · 2025Article
- Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.bioRxiv : the preprint server for biology · 2025Article
- Gut phages and their interactions with bacterial and mammalian hosts.Journal of bacteriology · 2025Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.
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