ArticleNature communications2022
Short- and long-read metagenomics expand individualized structural variations in gut microbiomes.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- Parallel evolution of chimeric genes in microbial evolution experiments.Microbial genomics · 2026Article
- Microbiome and aging: Trajectories of microbiome age across human ecosystems and their systemic effects.iMeta · 2026Review
- Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.Cell host & microbe · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.Applied and environmental microbiology · 2026Article
- Establishment of the chromid database and analysis of evolutionary research.Molecular genetics and genomics : MGG · 2026Article
- Seasonal life stage changes contribute to gut bacterial community profiles of high-altitude birds.Current zoology · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- Review
- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
- Article
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- Long-read sequencing for cancer liquid biopsy: advancing precision oncology.Frontiers in oncology · 2026Review
- Host-gut microbiota interactions in health and disease: mechanisms and intervention strategies.Frontiers in microbiology · 2026Review
- Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis.Nature communications · 2025Article
- Evaluation of metagenome binning: advances and challenges.Briefings in bioinformatics · 2025Article
- Convergent genomic responses of human gut bacteria to variations in industrialization.bioRxiv : the preprint server for biology · 2025Article
14 more citing papers are in PubMed but not listed here.
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19 authors.
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No grant is acknowledged in the PubMed record.
Abstract
In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome.
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