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

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

Journal: Genome biology
DOI: 10.1186/s13059-019-1760-x
Year: 2019

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