ArticleScientific reports2019
A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- Impact of phage enrichment on the observed infant gut phageome.Microbiology spectrum · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.bioRxiv : the preprint server for biology · 2025Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.bioRxiv : the preprint server for biology · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- A plasmid-chromosome crosstalk in multidrug resistant enterobacteria.Nature communications · 2024Article
- Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.Microbiome · 2024Article
- Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.Science advances · 2024Article
- Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Article
- Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome.Journal of advanced research · 2023Article
- Review
- Morphological and Genetic Characterization ofViruses · 2022Article
- Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies.Gut pathogens · 2022Article
- The gut virome in two indigenous populations from Malaysia.Scientific reports · 2022Article
- Bacteriophages Roam the Wheat Phyllosphere.Viruses · 2022Article
- In Silico Characterisation of Putative Prophages inMicroorganisms · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The microbiota of the human gut is a complex and rich community where bacteria and their viruses, the bacteriophages, are dominant. There are few studies on the phage community and no clear standard for isolating them, sequencing and analysing their genomes. Since this makes comparisons between studies difficult, we aimed at defining an easy, low-cost, and reproducible methodology. We analysed five different techniques to isolate phages from human adult faeces and developed an approach to analyse their genomes in order to quantify contamination and classify phage contigs in terms of taxonomy and lifestyle. We chose the polyethylene glycol concentration method to isolate phages because of its simplicity, low cost, reproducibility, and of the high number and diversity of phage sequences that we obtained. We also tested the reproducibility of this method with multiple displacement amplification (MDA) and showed that MDA severely decreases the phage genetic diversity of the samples and the reproducibility of the method. Lastly, we studied the influence of sequencing depth on the analysis of phage diversity and observed the beginning of a plateau for phage contigs at 20,000,000 reads. This work contributes to the development of methods for the isolation of phages in faeces and for their comparative analysis.
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