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Genome Biol. 2019 Aug 2;20(1):153. doi: 10.1186/s13059-019-1760-x.

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

Author information

1
Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA.
2
Division of Genetics and Genomics, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK.
3
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
4
Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA.
5
Phase Genomics Inc, Seattle, WA, 98109, USA.
6
Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
7
Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
8
Pacific Biosciences, Menlo Park, CA, USA.
9
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
10
Department of Animal Science, University of Tennessee, Knoxville, TN, 37996, USA.
11
Department of Computer Science, University of Maryland, College Park, MD, 20742, USA.
12
USDA-ARS U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA. tim.smith2@usda.gov.

Abstract

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.

KEYWORDS:

Hi-C; Metagenome assembly; Metagenomics; PacBio; Virus-host association

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