Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

Authors: Bickhart, Derek; WATSON, MICK - University Of Edinburgh; KOREN, SERGEY - National Institutes Of Health (NIH); Panke-Buisse, Kevin; CERSOSIMO, LAURA - University Of Florida; PRESS, MAXIMILLIAN - Phase Genomics, Inc; Van Tassell, Curtis - Curt; Van Kessel, Jo Ann; Haley, Bradd; KIM, SEON WOO - University Of Maryland; HEINER, CHERYL - Pacific Biosciences Inc; SUEN, GARRET - University Of Wisconsin; Bakshy, Kiranmayee; LIACHKO, IVAN - Phase Genomics, Inc; SULLIVAN, SHAWN - Phase Genomics, Inc; MYER, PHILLIP - University Of Tennessee; GHURYE, JAY - University Of Maryland; POP, MIHAI - University Of Maryland; WEIMER, PAUL - Retired ARS Employee; PHILLIPPY, ADAM - National Institutes Of Health (NIH); Smith, Timothy - Tim

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2019
Publication Date: 8/2/2019
Citation: Bickhart, D.M., Watson, M., Koren, S., Panke-Buisse, K., Cersosimo, L.M., Press, M.O., Van Tassell, C.P., Van Kessel, J.S., Haley, B.J., Kim, S., Heiner, C., Suen, G., Bakshy, K., Liachko, I., Sullivan, S.T., Myer, P.R., Ghurye, J., Pop, M., Weimer, P., Phillippy, A., Smith, T.P. 2019. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biology. 20:153. https://doi.org/10.1186/s13059-019-1760-x.
DOI: https://doi.org/10.1186/s13059-019-1760-x

Interpretive Summary: Viruses infect a wide array of cells and organisms, but it can sometimes be difficult to detect their hosts in microbial samples. We use improved methods to identify bacterial hosts of viruses in the cattle rumen and show that they play a major role in the community. Using our methods, it is also possible to distinguish the lifecycle of the virus in a complex sample. This information could be used to alter the rumen microbiome or to better understand rumen microbial data.

Technical Abstract: 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.