ArticleMicrobiome2019
Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 93 citations in OpenAlex.
- Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.Nature communications · 2026Review
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Decoding the human gut bacterial plasmids in colorectal cancer.Communications biology · 2026Article
- Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.Biology · 2026Review
- Review
- The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2026Review
- Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.NAR genomics and bioinformatics · 2025Article
- Next generation sequencing and beyond: a review of genomic sequencing methods.Functional & integrative genomics · 2025Article
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
- Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.Nature communications · 2025Article
- Article
- Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls.Scientific reports · 2025Article
- Alteration of salivaryFrontiers in pharmacology · 2025Article
- High-throughput single-cell sequencing of activated sludge microbiome.Environmental science and ecotechnology · 2025Article
- Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.Science advances · 2024Article
- Review
- Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.Communications biology · 2024Article
- Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.bioRxiv : the preprint server for biology · 2024Article
- Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.Microbiology spectrum · 2024Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundElucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity and diversity.
resultsHere, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), which were classified as 71 plasmids and 11 bacteriophages, including 58 novel plasmids and six bacteriophages, and complete genomes of five diverse crAssphages with terminal direct repeats. In a dataset of 413 gut metagenomes from five countries, many of the identified plasmids were highly abundant and prevalent. The ratio of gut plasmids by our plasmid data is more than twice that in the public database. Plasmids outnumbered bacterial chromosomes three to one on average in this metagenomic dataset. Host prediction suggested that Bacteroidetes-associated plasmids predominated, regardless of microbial abundance. The analysis found several plasmid-enriched functions, such as inorganic ion transport, while antibiotic resistance genes were harboured mostly in low-abundance Proteobacteria-associated plasmids.
conclusionsOverall, long-read metagenomics provided an efficient approach for unravelling the complete structure of human gut eMGEs, particularly plasmids.
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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.