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

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

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

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

Authors

Derek M Bickhart¹, Mick Watson², Sergey Koren³, Kevin Panke-Buisse¹, Laura M Cersosimo⁴, Maximilian O Press⁵, Curtis P Van Tassell⁶, Jo Ann S Van Kessel⁷, Bradd J Haley⁷, Seon Woo Kim⁷, Cheryl Heiner⁸, Garret Suen⁹, Kiranmayee Bakshy¹, Ivan Liachko⁵, Shawn T Sullivan⁵, Phillip R Myer¹⁰, Jay Ghurye¹¹, Mihai Pop¹¹, Paul J Weimer^{1

9}, Adam M Phillippy³, Timothy P L Smith¹²

Affiliations

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Cattle
Clustered Regularly Interspaced Short Palindromic Repeats
Drug Resistance, Microbial / genetics*
Gene Transfer, Horizontal
Genes, Microbial
Metagenomics / methods*
Microbiota / genetics*
Open Reading Frames
Prophages / genetics
Rumen / microbiology
Rumen / virology
Sequence Analysis, DNA / methods*
Viruses / genetics*
Viruses / isolation & purification

Abstract

Publication types

MeSH terms

Grants and funding