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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
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-h...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
BioMed Central
2019
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676630/ https://www.ncbi.nlm.nih.gov/pubmed/31375138 http://dx.doi.org/10.1186/s13059-019-1760-x |
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| author | Bickhart, Derek M. Watson, Mick Koren, Sergey Panke-Buisse, Kevin Cersosimo, Laura M. Press, Maximilian O. Van Tassell, Curtis P. Van Kessel, Jo Ann S. Haley, Bradd J. Kim, Seon Woo Heiner, Cheryl Suen, Garret Bakshy, Kiranmayee Liachko, Ivan Sullivan, Shawn T. Myer, Phillip R. Ghurye, Jay Pop, Mihai Weimer, Paul J. Phillippy, Adam M. Smith, Timothy P. L. |
| author_facet | Bickhart, Derek M. Watson, Mick Koren, Sergey Panke-Buisse, Kevin Cersosimo, Laura M. Press, Maximilian O. Van Tassell, Curtis P. Van Kessel, Jo Ann S. Haley, Bradd J. Kim, Seon Woo Heiner, Cheryl Suen, Garret Bakshy, Kiranmayee Liachko, Ivan Sullivan, Shawn T. Myer, Phillip R. Ghurye, Jay Pop, Mihai Weimer, Paul J. Phillippy, Adam M. Smith, Timothy P. L. |
| author_sort | Bickhart, Derek M. |
| collection | PubMed |
| description | 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. |
| format | Online Article Text |
| id | pubmed-6676630 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2019 |
| publisher | BioMed Central |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-66766302019-08-06 Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation Bickhart, Derek M. Watson, Mick Koren, Sergey Panke-Buisse, Kevin Cersosimo, Laura M. Press, Maximilian O. Van Tassell, Curtis P. Van Kessel, Jo Ann S. Haley, Bradd J. Kim, Seon Woo Heiner, Cheryl Suen, Garret Bakshy, Kiranmayee Liachko, Ivan Sullivan, Shawn T. Myer, Phillip R. Ghurye, Jay Pop, Mihai Weimer, Paul J. Phillippy, Adam M. Smith, Timothy P. L. Genome Biol Method 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. BioMed Central 2019-08-02 /pmc/articles/PMC6676630/ /pubmed/31375138 http://dx.doi.org/10.1186/s13059-019-1760-x Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
| spellingShingle | Method Bickhart, Derek M. Watson, Mick Koren, Sergey Panke-Buisse, Kevin Cersosimo, Laura M. Press, Maximilian O. Van Tassell, Curtis P. Van Kessel, Jo Ann S. Haley, Bradd J. Kim, Seon Woo Heiner, Cheryl Suen, Garret Bakshy, Kiranmayee Liachko, Ivan Sullivan, Shawn T. Myer, Phillip R. Ghurye, Jay Pop, Mihai Weimer, Paul J. Phillippy, Adam M. Smith, Timothy P. L. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation |
| title | Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation |
| title_full | Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation |
| title_fullStr | Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation |
| title_full_unstemmed | Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation |
| title_short | Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation |
| title_sort | assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation |
| topic | Method |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676630/ https://www.ncbi.nlm.nih.gov/pubmed/31375138 http://dx.doi.org/10.1186/s13059-019-1760-x |
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