期刊
NATURE BIOTECHNOLOGY
卷 38, 期 6, 页码 701-+出版社
NATURE PORTFOLIO
DOI: 10.1038/s41587-020-0422-6
关键词
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资金
- National Science Foundation [DGE-114747]
- Stanford Graduate Fellowships in Science and Engineering program
- Damon Runyon Clinical investigator award
- NIH [P30 CA124435, 1S10OD02014101]
- [NIH R01AI148623]
- [NIH P30 AG047366]
Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect of genome structure on genome function. We applied nanopore sequencing and our workflow, named Lathe, which incorporates long-read assembly and short-read error correction, to assemble closed bacterial genomes from complex microbiomes. We validated our approach with a synthetic mixture of 12 bacterial species. Seven genomes were completely assembled into single contigs and three genomes were assembled into four or fewer contigs. Next, we used our methods to analyze metagenomics data from 13 human stool samples. We assembled 20 circular genomes, including genomes of Prevotella copri and a candidate Cibiobacter sp. Despite the decreased nucleotide accuracy compared with alternative sequencing and assembly approaches, our methods improved assembly contiguity, allowing for investigation of the role of repeat elements in microbial function and adaptation. Nanopore-metagenomics workflow enables assembly of complete, closed bacterial genomes from human stool samples.
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