ArticleNature biotechnology2018
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.
Article in Nature biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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
94 citing papers in PubMed, 155 citations in OpenAlex.
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- Nanopore metagenomic sequencing links clinically relevant resistance determinants to pathogens.Microbial genomics · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 2026Article
- Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.Journal of bacteriology · 2026Review
- Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.Genome biology · 2026Article
- Comparative genomics and methylome profiling ofMicrobial genomics · 2026Article
- 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
- Draft genome sequence CR-NGP1 strain of 'Candidatus Liberibacter asiaticus' (CLas) from the host Citrus reticulata (Nagpur mandarin) from Central India.World journal of microbiology & biotechnology · 2026Article
- Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.Antibiotics (Basel, Switzerland) · 2026Review
- Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.mSystems · 2026Article
- Review
- Sulfonamide resistance geneMicrobiology spectrum · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Assessing live microbial therapeutic transmission.Gut microbes · 2025Review
- Precise virulence inactivation using a CRISPR-associated transposase for combating Enterobacteriaceae gut pathogens.Nature biomedical engineering · 2025Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Bacterial immune systems as causes and consequences of microbiome structure.PLoS biology · 2025Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.bioRxiv : the preprint server for biology · 2025Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.
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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.