Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
| Autor: | Kiranmayee Bakshy, Mick Watson, Jay Ghurye, Laura M. Cersosimo, Adam M. Phillippy, Seon Woo Kim, Sergey Koren, Bradd J. Haley, Cheryl Heiner, Maximilian O. Press, Garret Suen, Kevin Panke-Buisse, Curtis P. Van Tassell, Phillip R. Myer, Shawn T. Sullivan, Jo Ann S. Van Kessel, Mihai Pop, Paul J. Weimer, Ivan Liachko, Timothy P L Smith, Derek M. Bickhart |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Rumen
lcsh:QH426-470 Gene Transfer Horizontal Prophages Method Computational biology Biology Virus Open Reading Frames 03 medical and health sciences 0302 clinical medicine Hi-C Animals Clustered Regularly Interspaced Short Palindromic Repeats lcsh:QH301-705.5 030304 developmental biology PacBio 2. Zero hunger 0303 health sciences Contig Microbiota Drug Resistance Microbial Sequence Analysis DNA Short read Metagenome assembly lcsh:Genetics lcsh:Biology (General) Microbial population biology Metagenomics Virus-host association Viruses Antimicrobial resistance genes Cattle Identification (biology) Genes Microbial 030217 neurology & neurosurgery |
| Zdroj: | Bickhart, D M, Watson, M, Koren, S, Panke-Buisse, K, Cersosimo, L M, Press, M O, Van Tassell, C P, Van Kessel, J A S, Haley, B J, Kim, S W, Heiner, C, Suen, G, Bakshy, K, Liachko, I, Sullivan, S T, Myer, P R, Ghurye, J, Pop, M, Weimer, P J, Phillippy, A M & Smith, T P L 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, vol. 20, no. 1, pp. 153 . https://doi.org/10.1186/s13059-019-1760-x Genome Biology Genome Biology, Vol 20, Iss 1, Pp 1-18 (2019) |
| Popis: | 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. Electronic supplementary material The online version of this article (10.1186/s13059-019-1760-x) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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