RT Journal Article SR Electronic T1 Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation JF bioRxiv FD Cold Spring Harbor Laboratory SP 491175 DO 10.1101/491175 A1 Bickhart, Derek A1 Watson, Mick A1 Koren, Sergey A1 Panke-Buisse, Kevin A1 Cersosimo, Laura M A1 Press, Maximillian O A1 Van Tassell, Curtis P A1 Van Kessel, Jo Ann S A1 Haley, Bradd J A1 Kim, Seon Woo A1 Heiner, Cheryl A1 Suen, Garret A1 Bakshy, Kiranmayee A1 Liachko, Ivan A1 Sullivan, Shawn T A1 Ghurye, Jay A1 Pop, Mihai A1 Weimer, Paul J A1 Phillippy, Adam M A1 Smith, Timothy P.L. YR 2018 UL http://biorxiv.org/content/early/2018/12/09/491175.abstract AB The characterization of microbial communities by metagenomic approaches has been enhanced by recent improvements in short-read sequencing efficiency and assembly algorithms. We describe the results of adding long-read sequencing to the mix of technologies used to assemble a highly complex cattle rumen microbial community, and compare the assembly to current short read-based methods applied to the same sample. Contigs in the long-read assembly were 7-fold longer on average, and contained 7-fold more complete open reading frames (ORF), than the short read assembly, despite having three-fold lower sequence depth. The linkages between long-read contigs, provided by proximity ligation data, supported identification of 188 novel viral-host associations in the rumen microbial community that suggest cross-species infectivity of specific viral strains. The improved contiguity of the long-read assembly also identified 94 antimicrobial resistance genes, compared to only seven alleles identified in the short-read assembly. Overall, we demonstrate a combination of experimental and computational methods that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.