Dataset Information

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

ABSTRACT: We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

SUBMITTER: Bickhart DM

PROVIDER: S-EPMC6676630 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Bickhart Derek M DM Watson Mick M Koren Sergey S Panke-Buisse Kevin K Cersosimo Laura M LM Press Maximilian O MO Van Tassell Curtis P CP Van Kessel Jo Ann S JAS Haley Bradd J BJ Kim Seon Woo SW Heiner Cheryl C Suen Garret G Bakshy Kiranmayee K Liachko Ivan I Sullivan Shawn T ST Myer Phillip R PR Ghurye Jay J Pop Mihai M Weimer Paul J PJ Phillippy Adam M AM Smith Timothy P L TPL

Genome biology 20190802 1

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven all ...[more]

PMID: 31375138

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Dataset Information

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

Publications

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

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