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.