ArticleNature biotechnology2016
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome.
Article in Nature biotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
60 citing papers in PubMed.
- Human microbiome acquisition and transmission.Nature reviews. Microbiology · 2025Review
- Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.bioRxiv : the preprint server for biology · 2025Article
- Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.National science review · 2025Article
- Ecological Impacts of Sunflowers on Soil Microbial Communities: Insights from Full-Length 16S rRNA Sequencing.Current microbiology · 2025Article
- An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.Microbiology spectrum · 2024Article
- Research Progress of Buyang Yiwei Decoction in Regulating Intestinal Flora for Gastric Cancer.Cancer management and research · 2024Review
- Application of Microbiome in Forensics.Genomics, proteomics & bioinformatics · 2023Review
- Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Microbial characterization based on multifractal analysis of metagenomes.Frontiers in cellular and infection microbiology · 2023Article
- Profiling of d-alanine production by the microbial isolates of rat gut microbiota.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2022Article
- Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis.The Journal of pathology · 2022Review
- Pragmatic Expectancy on Microbiota and Non-Small Cell Lung Cancer: A Narrative Review.Cancers · 2022Review
- Generation and application of pseudo-long reads for metagenome assembly.GigaScience · 2022Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Examining horizontal gene transfer in microbial communities.Nature reviews. Microbiology · 2021Review
- Metagenome SNP calling via read-colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2021Article
- A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.Computational and structural biotechnology journal · 2021Review
- High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method.Microbiome · 2020Article
- Human microbiome: an academic update on human body site specific surveillance and its possible role.Archives of microbiology · 2020Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Identifying bacterial strains in metagenome and microbiome samples using computational analyses of short-read sequences remains a difficult problem. Here, we present an analysis of a human gut microbiome using TruSeq synthetic long reads combined with computational tools for metagenomic long-read assembly, variant calling and haplotyping (Nanoscope and Lens). Our analysis identifies 178 bacterial species, of which 51 were not found using shotgun reads alone. We recover bacterial contigs that comprise multiple operons, including 22 contigs of >1 Mbp. Furthermore, we observe extensive intraspecies variation within microbial strains in the form of haplotypes that span up to hundreds of Kbp. Incorporation of synthetic long-read sequencing technology with standard short-read approaches enables more precise and comprehensive analyses of metagenomic samples.
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Registered trials
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