PT - JOURNAL ARTICLE AU - Derek M. Bickhart AU - Mick Watson AU - Sergey Koren AU - Kevin Panke-Buisse AU - Laura M. Cersosimo AU - Maximilian O. Press AU - Curtis P. Van Tassell AU - Jo Ann S. Van Kessel AU - Bradd J. Haley AU - Seon Woo Kim AU - Cheryl Heiner AU - Garret Suen AU - Kiranmayee Bakshy AU - Ivan Liachko AU - Shawn T. Sullivan AU - Jay Ghurye AU - Mihai Pop AU - Paul J. Weimer AU - Adam M. Phillippy AU - Timothy P.L. Smith TI - Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation AID - 10.1101/491175 DP - 2018 Jan 01 TA - bioRxiv PG - 491175 4099 - http://biorxiv.org/content/early/2018/12/09/491175.short 4100 - http://biorxiv.org/content/early/2018/12/09/491175.full 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.