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

Derek M Bickhart, Mick Watson, Sergey Koren, Kevin Panke-Buisse, Laura M Cersosimo, Maximilian O Press, Curtis P Van Tassell, Jo Ann S Van Kessel, Bradd J Haley, Seon Woo Kim, Cheryl Heiner, Garret Suen, Kiranmayee Bakshy, Ivan Liachko, Shawn T Sullivan, Phillip R Myer, Jay Ghurye, Mihai Pop, Paul J Weimer, Adam M PhillippyTimothy P L Smith

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)153
JournalGenome Biology
Volume20
Issue number1
DOIs
Publication statusPublished - 2 Aug 2019

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