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Freshwater monitoring by nanopore sequencing

Urban, Lara; Holzer, Andre; Baronas, J Jotautas; Hall, Michael B; Braeuninger-Weimer, Philipp; Scherm, Michael J; Kunz, Daniel J; Perera, Surangi N; Martin-Herranz, Daniel E; Tipper, Edward T; Salter, Susannah J; Stammnitz, Maximilian R


Lara Urban

Andre Holzer

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


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.


Urban, L., Holzer, A., Baronas, J. J., Hall, M. B., Braeuninger-Weimer, P., Scherm, M. J., …Stammnitz, M. R. (2021). Freshwater monitoring by nanopore sequencing. eLife, 10,

Journal Article Type Article
Acceptance Date Dec 1, 2020
Online Publication Date Jan 19, 2021
Publication Date Jan 19, 2021
Deposit Date Dec 12, 2023
Journal eLife
Publisher eLife Sciences Publications
Peer Reviewed Peer Reviewed
Volume 10
Keywords General Immunology and Microbiology; General Biochemistry, Genetics and Molecular Biology; General Medicine; General Neuroscience
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