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 - ROSLIN INSTITUTE; KOREN, SERGEY - NATIONAL INSTITUTES OF HEALTH (NIH); PRESS, MAXIMILLIAN - PHASE GENOMICS, INC; PHILLIPPY, ADAM - NATIONAL INSTITUTES OF HEALTH (NIH); Smith, Timothy - Tim

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/22/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary:

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 our work improving metagenomic assembly quality by adding long-read sequencing and proximity ligation to assemble a complex cattle rumen microbial sample, as well as comparing the assembly to current short read-based methods applied to the same sample. Contigs in the long-read assembly were on average seven-fold more contiguous, and contained seven-fold more complete open reading frames, than the short read assembly despite having three-fold lower sequence depth. The long-read dataset also showed a clear difference in the sampled GC% profile of the community relative to the short-read data, suggesting that there are biases present in short-read dataset with respect to community sampling. We then investigated the utility of longer reads in the identification of phage hosts in the community. The linkages between long-read contigs, provided by proximity ligation data and long-read alignment overlap, supported the identification of numerous novel species’ genomes as well as 188 novel host-viral associations in the rumen microbial community suggesting cross-species infectivity of specific viral strains. Identified host-viral associations were distinct between the two discovery methods and likely corresponded to the identification of lytic or lysogenic phage species, respectively. 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. These methods uncovered several features that were previously uncharacterized in the cattle rumen, suggesting that comprehensive approaches should be the standard for metagenomic surveys of complex communities. We also present a novel method to identify host associations with mobile genetic elements that is sensitive enough to determine the putative lifecycle of linked bacteriophages.