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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #362620

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

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

item Bickhart, Derek
item WATSON, MICK - Roslin Institute
item KOREN, SERGEY - National Institutes Of Health (NIH)
item PHILLIPPY, ADAM - National Institutes Of Health (NIH)
item Smith, Timothy - Tim

Submitted to: Cold Spring Harbor Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/3/2019
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 adding long-read sequencing to the mix of technologies used to assemble a complex cattle rumen microbial sample, 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. We also investigated the utility of longer reads in the identification of prophage hosts in the community. The linkages between long-read contigs, provided by proximity ligation data and long-read alignment overlap, supported identification of 188 novel viral-host associations in the rumen microbial community that suggest 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. Overall, we demonstrate a novel method for identifying host-viral associations in a complex microbial community that provides insights into the lifecycle of the virus and we show that a mix of different sequencing technologies is needed to identify all members of the community.