Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
oleh: 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. Phillippy, Timothy P. L. Smith
| Format: | Article |
|---|---|
| Diterbitkan: | BMC 2019-08-01 |
Deskripsi
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.