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

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 PhillippyTimothy P L Smith

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	153
Journal	Genome Biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1760-x
Publication status	Published - 2 Aug 2019

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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., ... 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, 20(1), 153. https://doi.org/10.1186/s13059-019-1760-x

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

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.",

author = "Bickhart, {Derek M} and Mick Watson and Sergey Koren and Kevin Panke-Buisse 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 Cheryl Heiner and Garret Suen and Kiranmayee Bakshy and Ivan Liachko and Sullivan, {Shawn T} and Myer, {Phillip R} and Jay Ghurye and Mihai Pop and Weimer, {Paul J} and Phillippy, {Adam M} and Smith, {Timothy P L}",

year = "2019",

month = aug,

day = "2",

doi = "10.1186/s13059-019-1760-x",

language = "English",

volume = "20",

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journal = "Genome Biology",

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publisher = "BioMed Central",

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Bickhart, DM, Watson, M, Koren, S, Panke-Buisse, K, Cersosimo, LM, Press, MO, Van Tassell, CP, Van Kessel, JAS, Haley, BJ, Kim, SW, Heiner, C, Suen, G, Bakshy, K, Liachko, I, Sullivan, ST, Myer, PR, Ghurye, J, Pop, M, Weimer, PJ, Phillippy, AM & Smith, TPL 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

TY - JOUR

T1 - Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

AU - Bickhart, Derek M

AU - Watson, Mick

AU - Koren, Sergey

AU - Panke-Buisse, Kevin

AU - Cersosimo, Laura M

AU - Press, Maximilian O

AU - Van Tassell, Curtis P

AU - Van Kessel, Jo Ann S

AU - Haley, Bradd J

AU - Kim, Seon Woo

AU - Heiner, Cheryl

AU - Suen, Garret

AU - Bakshy, Kiranmayee

AU - Liachko, Ivan

AU - Sullivan, Shawn T

AU - Myer, Phillip R

AU - Ghurye, Jay

AU - Pop, Mihai

AU - Weimer, Paul J

AU - Phillippy, Adam M

AU - Smith, Timothy P L

PY - 2019/8/2

Y1 - 2019/8/2

N2 - 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.

AB - 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.

U2 - 10.1186/s13059-019-1760-x

DO - 10.1186/s13059-019-1760-x

M3 - Article

C2 - 31375138

SN - 1465-6906

VL - 20

SP - 153

JO - Genome Biology

JF - Genome Biology

IS - 1

ER -

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

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