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 Derek M. Bickhart
A1 Mick Watson
A1 Sergey Koren
A1 Kevin Panke-Buisse
A1 Laura M. Cersosimo
A1 Maximilian O. Press
A1 Curtis P. Van Tassell
A1 Jo Ann S. Van Kessel
A1 Bradd J. Haley
A1 Seon Woo Kim
A1 Cheryl Heiner
A1 Garret Suen
A1 Kiranmayee Bakshy
A1 Ivan Liachko
A1 Shawn T. Sullivan
A1 Jay Ghurye
A1 Mihai Pop
A1 Paul J. Weimer
A1 Adam M. Phillippy
A1 Timothy P.L. Smith
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.