Year: 2020
Type: article
Abstract: 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.
Source: Nature Biotechnology
Authors: Eli L. Moss, Dylan G. Maghini, Ami S. Bhatt
Institutions: Stanford University, Stanford Medicine
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $12,690
Funders: National Science Foundation, U.S. Department of Health and Human Services, Damon Runyon Cancer Research Foundation, Stanford University, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Directorate for Education and Human Resources, National Institute on Aging, National Human Genome Research Institute, National Cancer Institute, National Institute of Allergy and Infectious Diseases, Division of Graduate Education, Stanford Cancer Institute
Awards: Emerging novel mechanisms of antibiotic resistance in the prevalent foodborne pathogen, Salmonella, G1868717214, G2086498705, G2649945114, High-throughput sequencer for multi-scale genomic studies, G4475131919, Stanford Alzheimer's Disease Research Center, G4579858310, G4715141192, Culture-free pathogen tracking in hospitalized patients, G5097059376, G5388169339, G6382129581, G736622850, G9000212151, G9000219376, Stanford Cancer Institute, Institutional Training Grant in Genome Science, Stanford Alzheimer's Disease Research Center
OpenAlex ID: W3005528502