Published April 11, 2024 | Version v1
Dataset Open

Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts

Authors/Creators

  • 1. ROR icon Fudan University

Contributors

Data curator:

Description

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 employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant 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. Strikingly, 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 exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.

Notes (English)

The Chinese Human Gut Virome (CHGV) catalog we established previously (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA007087)  consists of 21,648 non-redundant phage genomes, and was assembled by using a hybrid pipeline that combined both short- (Illumina) and long- (PacBio) reads.

Notes (English)

Content

  • PBSV_pipeline.sh: Scripts for detecting phage structural variations across the CHGV cohort
  • Benchmarking_pipeline.sh: Generating sumulated virome-enriched metagenomics datasets with known introduced SVs and benchmarking different long-read based SV calling methods with PSDP pipeline.
  • Analysis_script/PhageSV_quality_Part1.R: Overview of 14,438 non-redundant structural variants (SVs) in the human gut phageome.
  • Analysis_script/Functional_enrichment_analysis.py: Functional enrichment analysis of phage SVs.
  • Analysis_script/PhageSV_function.R: Visualization of enriched functions in phage SVs.
  • Analysis_script/PhageSV_GE.R: Bacteria-to-phage HGT analysis
  • Analysis_script/PhageSV_BVinteraction.R: Bactera-phage SV sharing network
  • Analysis_script/PhageSV_Phage_host_GE_analysis.R: Phage-host genetical interaction analysis

Data

  • Results/Sample_SV_common_0.8_suppl.vcf: 14,334 non-redundant VCF file
  • Results/SV_bed_inf.tsv: Viral SV information extracted from non-redundant VCF file
  • Results/all_genome_SNP_inf.tsv: SNV for each viral contig extracted from the output file of inStrain
  • Results/all_gene_SNP_inf.tsv: SNV for each viral gene extracted from the output file of inStrain
  • ViralSV_density_inf: SV density per viral_contig per sample, taxonomy, Temperate lifestyle
 

Files

PhageSV.zip

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Additional details

Dates

Available
2024

Software

Repository URL
https://github.com/ZhaoXM-Lab/PhageSV
Programming language
Python , R
Development Status
Active