ArticleNature biotechnology2022
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed.
- Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.Journal of advanced research · 2026Article
- Article
- CAMEO: a CAZyme mapping engine optimized for HUMAnN.Microbiology resource announcements · 2026Article
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.Journal of bacteriology · 2026Review
- Maternal and infant gut microbiome.iMeta · 2026Review
- Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.Nature biotechnology · 2026Article
- VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.Bioinformatics (Oxford, England) · 2026Article
- Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.Science China. Life sciences · 2026Article
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- Improving metagenome binning by integrating intrinsic features and taxonomy.Nature biotechnology · 2026Article
- Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.bioRxiv : the preprint server for biology · 2026Article
- Holo-2bRAD: A Hologenomic Method for High-Resolution Analysis of Coral Microbiomes During Bleaching.Microorganisms · 2026Article
- Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.Environmental microbiome · 2026Article
- Review
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.Environmental science and ecotechnology · 2026Article
- Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.mSystems · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
65 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.
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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.