MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research
In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Water |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4441/14/16/2491 |
| _version_ | 1797441264058105856 |
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| author | David Werner Kishor Acharya Adrian Blackburn Rixia Zan Jidapa Plaimart Ben Allen Shaaban Mrisho Mgana Shadrack Mwita Sabai Franella Francos Halla Said Maneno Massawa Alemseged Tamiru Haile Andualem Mekonnen Hiruy Jemila Mohammed Soydoa Vinitnantharat Thunchanok Thongsamer Kalyan Pantha Cesar Rossas Mota Filho Bruna Coelho Lopes |
| author_facet | David Werner Kishor Acharya Adrian Blackburn Rixia Zan Jidapa Plaimart Ben Allen Shaaban Mrisho Mgana Shadrack Mwita Sabai Franella Francos Halla Said Maneno Massawa Alemseged Tamiru Haile Andualem Mekonnen Hiruy Jemila Mohammed Soydoa Vinitnantharat Thunchanok Thongsamer Kalyan Pantha Cesar Rossas Mota Filho Bruna Coelho Lopes |
| author_sort | David Werner |
| collection | DOAJ |
| description | In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications. |
| first_indexed | 2024-03-09T12:21:31Z |
| format | Article |
| id | doaj.art-1eb26971ea5841118d3436d45637134e |
| institution | Directory Open Access Journal |
| issn | 2073-4441 |
| language | English |
| last_indexed | 2024-03-09T12:21:31Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Water |
| spelling | doaj.art-1eb26971ea5841118d3436d45637134e2023-11-30T22:40:19ZengMDPI AGWater2073-44412022-08-011416249110.3390/w14162491MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water ResearchDavid Werner0Kishor Acharya1Adrian Blackburn2Rixia Zan3Jidapa Plaimart4Ben Allen5Shaaban Mrisho Mgana6Shadrack Mwita Sabai7Franella Francos Halla8Said Maneno Massawa9Alemseged Tamiru Haile10Andualem Mekonnen Hiruy11Jemila Mohammed12Soydoa Vinitnantharat13Thunchanok Thongsamer14Kalyan Pantha15Cesar Rossas Mota Filho16Bruna Coelho Lopes17School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UKSchool of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UKSchool of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UKSchool of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UKSchool of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UKSchool of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UKDepartment of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam P.O. Box 35176, TanzaniaDepartment of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam P.O. Box 35176, TanzaniaDepartment of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam P.O. Box 35176, TanzaniaDepartment of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam P.O. Box 35176, TanzaniaInternational Water Management Institute (IWMI), Addis Ababa P.O. Box 5689, EthiopiaCenter for Environmental Science, Addis Ababa University, Addis Ababa P.O. Box 33348, EthiopiaAddis Ababa Water and Sewerage Authority (AAWSA), Addis Ababa P.O. Box 1505, EthiopiaEnvironmental Technology Program, School of Energy, Environment and Materials, King Mongkut’s University of Technology Thonburi, Bangkok 10140, ThailandEnvironmental Technology Program, School of Energy, Environment and Materials, King Mongkut’s University of Technology Thonburi, Bangkok 10140, ThailandGroup for Rural Infrastructure Development, Wise Use House, G.P.O. Box 7731, Jwagal, Lalitpur, NepalDepartment of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, BrazilDepartment of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte 31270-010, BrazilIn 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications.https://www.mdpi.com/2073-4441/14/16/2491MinIONnanopore sequencingNGSeDNAwater researchubiquitous genetics |
| spellingShingle | David Werner Kishor Acharya Adrian Blackburn Rixia Zan Jidapa Plaimart Ben Allen Shaaban Mrisho Mgana Shadrack Mwita Sabai Franella Francos Halla Said Maneno Massawa Alemseged Tamiru Haile Andualem Mekonnen Hiruy Jemila Mohammed Soydoa Vinitnantharat Thunchanok Thongsamer Kalyan Pantha Cesar Rossas Mota Filho Bruna Coelho Lopes MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research Water MinION nanopore sequencing NGS eDNA water research ubiquitous genetics |
| title | MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research |
| title_full | MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research |
| title_fullStr | MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research |
| title_full_unstemmed | MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research |
| title_short | MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research |
| title_sort | minion nanopore sequencing accelerates progress towards ubiquitous genetics in water research |
| topic | MinION nanopore sequencing NGS eDNA water research ubiquitous genetics |
| url | https://www.mdpi.com/2073-4441/14/16/2491 |
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