학술논문
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Document Type
Article
Author
Bickhart, Derek; Watson, Mick; Koren, Sergey; Panke-Buisse, Kevin; Cersosimo, Laura; Press, Maximilian; Tassell, Curtis; Kessel, Jo; Haley, Bradd; Kim, Seon; Heiner, Cheryl; Suen, Garret; Bakshy, Kiranmayee; Liachko, Ivan; Sullivan, Shawn; Myer, Phillip; Ghurye, Jay; Pop, Mihai; Weimer, Paul; Phillippy, Adam; Smith, Timothy
Source
Genome Biology; December 2019, Vol. 20 Issue: 1 p1-18, 18p
Subject
Language
ISSN
14747596; 1474760X
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.