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...
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| Published in | eLife Vol. 10 |
|---|---|
| Main Authors | , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
eLife Science Publications, Ltd
19.01.2021
eLife Sciences Publications Ltd eLife Sciences Publications, Ltd |
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| Online Access | Get full text |
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| 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.
Many water-dwelling bacteria can cause severe diseases such as cholera, typhoid or leptospirosis. One way to prevent outbreaks is to test water sources to find out which species of microbes they contain, and at which levels.
Traditionally, this involves taking a water sample, followed by growing a few species of ‘indicator bacteria’ that help to estimate whether the water is safe. An alternative technique, called metagenomics, has been available since the mid-2000s. It consists in reviewing (or ‘sequencing’) the genetic information of most of the bacteria present in the water, which allows scientists to spot harmful species. Both methods, however, require well-equipped laboratories with highly trained staff, making them challenging to use in remote areas.
The MinION is a pocket-sized device that – when paired with a laptop or mobile phone – can sequence genetic information ‘on the go’. It has already been harnessed during Ebola, Zika or SARS-CoV-2 epidemics to track the genetic information of viruses in patients and environmental samples. However, it is still difficult to use the MinION and other sequencers to monitor bacteria in water sources, partly because the genetic information of the microbes is highly fragmented during DNA extraction.
To address this challenge, Urban, Holzer et al. set out to optimise hardware and software protocols so the MinION could be used to detect bacterial species present in rivers. The tests focussed on the River Cam in Cambridge, UK, a waterway which faces regular public health problems: local rowers and swimmers often contract waterborne infections, sometimes leading to river closures.
For six months, Urban, Holzer et al. used the MinION to map out the bacteria present across nine river sites, assessing the diversity of species and the presence of disease-causing microbes in the water. In particular, the results showed that optimising the protocols made it possible to tell the difference between closely related species – an important feature since harmful and inoffensive bacteria can sometimes be genetically close. The data also revealed that the levels of harmful bacteria were highest downstream of urban river sections, near a water treatment plant and river barge moorings. Together, these findings demonstrate that optimising MinION protocols can turn this device into a useful tool to easily monitor water quality.
Around the world, climate change, rising urbanisation and the intensification of agriculture all threaten water quality. In fact, access to clean water is one of the United Nations sustainable development goals for 2030. Using the guidelines developed by Urban, Holzer et al., communities could harness the MinION to monitor water quality in remote areas, offering a cost-effective, portable DNA analysis tool to protect populations against deadly diseases. |
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| AbstractList | 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. 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. eLife digest Many water-dwelling bacteria can cause severe diseases such as cholera, typhoid or leptospirosis. One way to prevent outbreaks is to test water sources to find out which species of microbes they contain, and at which levels. Traditionally, this involves taking a water sample, followed by growing a few species of 'indicator bacteria' that help to estimate whether the water is safe. An alternative technique, called metagenomics, has been available since the mid-2000s. It consists in reviewing (or 'sequencing') the genetic information of most of the bacteria present in the water, which allows scientists to spot harmful species. Both methods, however, require well-equipped laboratories with highly trained staff, making them challenging to use in remote areas. The MinION is a pocket-sized device that -- when paired with a laptop or mobile phone -- can sequence genetic information 'on the go'. It has already been harnessed during Ebola, Zika or SARS-CoV-2 epidemics to track the genetic information of viruses in patients and environmental samples. However, it is still difficult to use the MinION and other sequencers to monitor bacteria in water sources, partly because the genetic information of the microbes is highly fragmented during DNA extraction. To address this challenge, Urban, Holzer et al. set out to optimise hardware and software protocols so the MinION could be used to detect bacterial species present in rivers. The tests focussed on the River Cam in Cambridge, UK, a waterway which faces regular public health problems: local rowers and swimmers often contract waterborne infections, sometimes leading to river closures. For six months, Urban, Holzer et al. used the MinION to map out the bacteria present across nine river sites, assessing the diversity of species and the presence of disease-causing microbes in the water. In particular, the results showed that optimising the protocols made it possible to tell the difference between closely related species -- an important feature since harmful and inoffensive bacteria can sometimes be genetically close. The data also revealed that the levels of harmful bacteria were highest downstream of urban river sections, near a water treatment plant and river barge moorings. Together, these findings demonstrate that optimising MinION protocols can turn this device into a useful tool to easily monitor water quality. Around the world, climate change, rising urbanisation and the intensification of agriculture all threaten water quality. In fact, access to clean water is one of the United Nations sustainable development goals for 2030. Using the guidelines developed by Urban, Holzer et al., communities could harness the MinION to monitor water quality in remote areas, offering a cost-effective, portable DNA analysis tool to protect populations against deadly diseases. 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. Many water-dwelling bacteria can cause severe diseases such as cholera, typhoid or leptospirosis. One way to prevent outbreaks is to test water sources to find out which species of microbes they contain, and at which levels. Traditionally, this involves taking a water sample, followed by growing a few species of ‘indicator bacteria’ that help to estimate whether the water is safe. An alternative technique, called metagenomics, has been available since the mid-2000s. It consists in reviewing (or ‘sequencing’) the genetic information of most of the bacteria present in the water, which allows scientists to spot harmful species. Both methods, however, require well-equipped laboratories with highly trained staff, making them challenging to use in remote areas. The MinION is a pocket-sized device that – when paired with a laptop or mobile phone – can sequence genetic information ‘on the go’. It has already been harnessed during Ebola, Zika or SARS-CoV-2 epidemics to track the genetic information of viruses in patients and environmental samples. However, it is still difficult to use the MinION and other sequencers to monitor bacteria in water sources, partly because the genetic information of the microbes is highly fragmented during DNA extraction. To address this challenge, Urban, Holzer et al. set out to optimise hardware and software protocols so the MinION could be used to detect bacterial species present in rivers. The tests focussed on the River Cam in Cambridge, UK, a waterway which faces regular public health problems: local rowers and swimmers often contract waterborne infections, sometimes leading to river closures. For six months, Urban, Holzer et al. used the MinION to map out the bacteria present across nine river sites, assessing the diversity of species and the presence of disease-causing microbes in the water. In particular, the results showed that optimising the protocols made it possible to tell the difference between closely related species – an important feature since harmful and inoffensive bacteria can sometimes be genetically close. The data also revealed that the levels of harmful bacteria were highest downstream of urban river sections, near a water treatment plant and river barge moorings. Together, these findings demonstrate that optimising MinION protocols can turn this device into a useful tool to easily monitor water quality. Around the world, climate change, rising urbanisation and the intensification of agriculture all threaten water quality. In fact, access to clean water is one of the United Nations sustainable development goals for 2030. Using the guidelines developed by Urban, Holzer et al., communities could harness the MinION to monitor water quality in remote areas, offering a cost-effective, portable DNA analysis tool to protect populations against deadly diseases. 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.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. |
| Audience | Academic |
| Author | Hall, Michael B Holzer, Andre Martin-Herranz, Daniel E Braeuninger-Weimer, Philipp Perera, Surangi N Scherm, Michael J Baronas, J Jotautas Kunz, Daniel J Salter, Susannah J Urban, Lara Tipper, Edward T Stammnitz, Maximilian R |
| Author_xml | – sequence: 1 givenname: Lara orcidid: 0000-0002-5445-9314 surname: Urban fullname: Urban, Lara organization: European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom – sequence: 2 givenname: Andre orcidid: 0000-0003-2439-6364 surname: Holzer fullname: Holzer, Andre organization: Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom – sequence: 3 givenname: J Jotautas orcidid: 0000-0002-4027-3965 surname: Baronas fullname: Baronas, J Jotautas organization: Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom – sequence: 4 givenname: Michael B orcidid: 0000-0003-3683-6208 surname: Hall fullname: Hall, Michael B organization: European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom – sequence: 5 givenname: Philipp orcidid: 0000-0001-8677-1647 surname: Braeuninger-Weimer fullname: Braeuninger-Weimer, Philipp organization: Department of Engineering, University of Cambridge, Cambridge, United Kingdom – sequence: 6 givenname: Michael J orcidid: 0000-0002-3289-9159 surname: Scherm fullname: Scherm, Michael J organization: Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom – sequence: 7 givenname: Daniel J orcidid: 0000-0003-3597-6591 surname: Kunz fullname: Kunz, Daniel J organization: Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom, Department of Physics, University of Cambridge, Cambridge, United Kingdom – sequence: 8 givenname: Surangi N orcidid: 0000-0003-4827-9242 surname: Perera fullname: Perera, Surangi N organization: Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, United Kingdom – sequence: 9 givenname: Daniel E orcidid: 0000-0002-2285-3317 surname: Martin-Herranz fullname: Martin-Herranz, Daniel E organization: European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom – sequence: 10 givenname: Edward T orcidid: 0000-0003-3540-3558 surname: Tipper fullname: Tipper, Edward T organization: Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom – sequence: 11 givenname: Susannah J orcidid: 0000-0003-3898-8504 surname: Salter fullname: Salter, Susannah J organization: Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom – sequence: 12 givenname: Maximilian R orcidid: 0000-0002-1704-9199 surname: Stammnitz fullname: Stammnitz, Maximilian R organization: Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33461660$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | 2021, Urban et al. COPYRIGHT 2021 eLife Science Publications, Ltd. 2021, Urban et al. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2021, Urban et al 2021 Urban et al |
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| DOI | 10.7554/eLife.61504 |
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| Keywords | bacterial monitoring computational biology environmental metagenomics nanopore sequencing ecology infectious disease microbiology portable dna analysis freshwater ecology |
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| SubjectTerms | Aquatic resources Bacteria Bacteria - classification Bacteria - genetics bacterial monitoring Base Sequence Bioinformatics Cholera Classification Cluster Analysis computational biology Computational Biology - methods DNA sequencing Ecology environmental metagenomics Environmental monitoring Environmental Monitoring - methods Epidemics Fresh Water - microbiology freshwater ecology Geography Global temperature changes Health aspects Indicator species Indicators (Biology) Laboratories Metagenome - genetics Metagenomics Metagenomics - methods Microbiology and Infectious Disease Microbiomes Microbiota Microbiota (Symbiotic organisms) Microbiota - genetics nanopore sequencing Nanopore Sequencing - methods Nucleotide sequencing Pathogens portable dna analysis Public health Rivers Rivers - microbiology RNA, Ribosomal, 16S - genetics Sequence Homology, Nucleic Acid Sewage Species Specificity Surface water Surveys Taxonomy Tropical diseases United Kingdom Water Microbiology Waterborne diseases Waterborne infections |
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| Title | Freshwater monitoring by nanopore sequencing |
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