Freshwater monitoring by nanopore sequencing
While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2021-01-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/61504 |
| _version_ | 1828221534889574400 |
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| author | Lara Urban Andre Holzer J Jotautas Baronas Michael B Hall Philipp Braeuninger-Weimer Michael J Scherm Daniel J Kunz Surangi N Perera Daniel E Martin-Herranz Edward T Tipper Susannah J Salter Maximilian R Stammnitz |
| author_facet | Lara Urban Andre Holzer J Jotautas Baronas Michael B Hall Philipp Braeuninger-Weimer Michael J Scherm Daniel J Kunz Surangi N Perera Daniel E Martin-Herranz Edward T Tipper Susannah J Salter Maximilian R Stammnitz |
| author_sort | Lara Urban |
| collection | DOAJ |
| description | While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices. |
| first_indexed | 2024-04-12T16:42:32Z |
| format | Article |
| id | doaj.art-a5cdef33d3f84e9d9243d7fba7dc42b4 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:42:32Z |
| publishDate | 2021-01-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-a5cdef33d3f84e9d9243d7fba7dc42b42022-12-22T03:24:43ZengeLife Sciences Publications LtdeLife2050-084X2021-01-011010.7554/eLife.61504Freshwater monitoring by nanopore sequencingLara Urban0https://orcid.org/0000-0002-5445-9314Andre Holzer1https://orcid.org/0000-0003-2439-6364J Jotautas Baronas2https://orcid.org/0000-0002-4027-3965Michael B Hall3https://orcid.org/0000-0003-3683-6208Philipp Braeuninger-Weimer4https://orcid.org/0000-0001-8677-1647Michael J Scherm5https://orcid.org/0000-0002-3289-9159Daniel J Kunz6https://orcid.org/0000-0003-3597-6591Surangi N Perera7https://orcid.org/0000-0003-4827-9242Daniel E Martin-Herranz8https://orcid.org/0000-0002-2285-3317Edward T Tipper9https://orcid.org/0000-0003-3540-3558Susannah J Salter10https://orcid.org/0000-0003-3898-8504Maximilian R Stammnitz11https://orcid.org/0000-0002-1704-9199European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United KingdomDepartment of Plant Sciences, University of Cambridge, Cambridge, United KingdomDepartment of Earth Sciences, University of Cambridge, Cambridge, United KingdomEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United KingdomDepartment of Engineering, University of Cambridge, Cambridge, United KingdomDepartment of Biochemistry, University of Cambridge, Cambridge, United KingdomWellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom; Department of Physics, University of Cambridge, Cambridge, United KingdomDepartment of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, United KingdomEuropean Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United KingdomDepartment of Earth Sciences, University of Cambridge, Cambridge, United KingdomDepartment of Veterinary Medicine, University of Cambridge, Cambridge, United KingdomDepartment of Veterinary Medicine, University of Cambridge, Cambridge, United KingdomWhile traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.https://elifesciences.org/articles/61504nanopore sequencingenvironmental metagenomicsfreshwater ecologybacterial monitoringportable dna analysiscomputational biology |
| spellingShingle | Lara Urban Andre Holzer J Jotautas Baronas Michael B Hall Philipp Braeuninger-Weimer Michael J Scherm Daniel J Kunz Surangi N Perera Daniel E Martin-Herranz Edward T Tipper Susannah J Salter Maximilian R Stammnitz Freshwater monitoring by nanopore sequencing eLife nanopore sequencing environmental metagenomics freshwater ecology bacterial monitoring portable dna analysis computational biology |
| title | Freshwater monitoring by nanopore sequencing |
| title_full | Freshwater monitoring by nanopore sequencing |
| title_fullStr | Freshwater monitoring by nanopore sequencing |
| title_full_unstemmed | Freshwater monitoring by nanopore sequencing |
| title_short | Freshwater monitoring by nanopore sequencing |
| title_sort | freshwater monitoring by nanopore sequencing |
| topic | nanopore sequencing environmental metagenomics freshwater ecology bacterial monitoring portable dna analysis computational biology |
| url | https://elifesciences.org/articles/61504 |
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