Freshwater monitoring by nanopore sequencing

ABSTRACT 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...

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Published inbioRxiv
Main Authors Urban, Lara, Holzer, Andre, Baronas, J Jotautas, Hall, Michael, 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
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 18.11.2020
Cold Spring Harbor Laboratory
Edition1.6
Subjects
Bacteria
Computer applications
Deoxyribonucleic acid
DNA
DNA sequencing
Metagenomics
Microbiology
Microbiota
Pathogens
Public health
Rivers
Surface water
environmental metagenomics
portable bacterial monitoring
Nanopore sequencing
freshwater ecology
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Summary:ABSTRACT 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. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://www.puntseq.co.uk/ * https://github.com/d-j-k/puntseq * https://www.ebi.ac.uk/ena/data/view/PRJEB34900
Bibliography:SourceType-Working Papers-1
ObjectType-Working Paper/Pre-Print-1
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Competing Interest Statement: The authors have declared no competing interest.
ISSN:2692-8205
2692-8205
DOI:10.1101/2020.02.06.936302