Environmental research and conservation
Portable and affordable nanopore sequencing technology delivers unique opportunities for environmental research. It has been used extensively to analyse environmental DNA (eDNA) and microbiome samples to support biodiversity assessment, ecosystem biomonitoring, pathogen identification, and animal conservation. Long nanopore reads provide enhanced species identification, while real-time data analysis delivers immediate access to results, whether in the field or in the lab.
Revolutionising biodiversity research: Oxford Nanopore sequencing for the rapid and accurate identification of endangered species
By enabling researchers to identify species rapidly and accurately, Oxford Nanopore may revolutionise the field of biodiversity research, especially ... in developing countries.
Mariana Corrales Orozco, EAFIT University, Colombia
Oxford Nanopore sequencing
Legacy short-read technologies
Flexible, portable, and scalable
- Sequence at source, even in the most extreme environments with the portable MinION device — minimising potential sample degradation caused by storage and shipping
- Sequence what you need with flexible end-to-end workflows that suit your output or input needs
- Scale up and sequence with high-output, modular GridION and PromethION devices
Limited flexibility
Legacy technologies are typically expensive and require high sample batching for optimal efficiency, delaying time to result. The benchtop devices are often bulky and need substantial site infrastructure, restricting its usage to well-resourced, centralised locations.
Real-time data streaming
- Analyse data and identify species as it is generated for rapid insights
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Use intuitive EPI2ME workflows for real-time microbiome analysis, including metagenomic- and 16S ribosomal RNA (rRNA)-based identification and quantification
Fixed run time with bulk data delivery
Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional complexities of handing large volumes of bulk data.
Unrestricted read length (>4 Mb achieved)
- Sequence the full-length 16S rRNA gene for enhanced taxonomic resolution
- Assemble complete genomes and plasmids from metagenomic samples — resolving similar species and complex genomic regions
Read length typically 50–300 bp
Short sequencing reads do not typically span complex genomic regions, reducing the contiguity of metagenome assemblies. Metabarcoding of specific regions of interest with short reads has been reported to provide limited phylogenetic resolution.
Streamlined workflows
- Sample prep in as little as 10 minutes and multiplex up to 96 samples in a single run
- Whole genome, metagenomic, targeted, direct RNA, cDNA, and 16S sequencing approaches are available
- Eliminate amplification- and GC-bias, and detect base modifications alongside nucleotide sequence with amplification-free protocols
Laborious workflows
Typically lengthy sample preparation requirements and long sequencing run times reduce workflow efficiency. Base modifications (e.g. methylation) are also not detected as standard, with extra preparation steps and additional sequencing runs required, further increasing turnaround times.
Addressing the challenges of metagenomics
Microbial communities can have a profound effect on their environment, for example breaking down pollutants, sequestering carbon, or generating useful by-products. In the same manner, environmental pressures, such as climate change, can impact the constitution of microbial communities. As a result, metagenomic analysis — the genomic investigation of multiple organisms from a single sample — reveals significant insights into the structure and function of microbial communities and can act as an environmental monitoring system. This white paper explores the challenges of metagenomics, with real-world examples of how they are now being addressed through the use of nanopore sequencing technology.
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Supporting rapid sequencing of critically endangered species, anywhere, by anyone
ORG.one is a pilot-stage project designed to support faster, more localised sequencing of critically endangered species, by enabling biologists to rapidly sequence those species close to the sample’s origin, using the latest ultra-long read approaches.
Data-rich, de novo whole-genome assemblies will be enabled through the provision of consumable support that can be used with Oxford Nanopore sequencers, on the condition that the data generated will be openly shared with the scientific community.
Cataloguing biodiversity to improve economic resilience
During the COVID-19 pandemic in 2020, tourism in the Galapagos islands plummeted with devastating effect on the population. At London Calling 2023, Jaime A. Chaves shares how his team used nanopore technology to create new employment opportunities to improve economic resilience whilst protecting the archipelago’s ecosystem.
The best example of how nanopore technologies … is democratising science
Jaime A. Chaves, San Francisco State University, USA
Endangered European sturgeon detection through non-amplified eDNA sequencing
Reindert Nijland and his lab have utilised the ORG.one initiative to sequence the critically endangered European sturgeon. As part of a reintroduction programme, the species needs to be tracked to monitor the success of the reintroduction compared with invasive species. Reindert shares how his team has helped develop an eDNA-based monitoring workflow to sequence the sturgeon species.
A really nice proof of concept ... we hope to extend to all fish species in the Netherlands ... for all marine species ... and to extend to [sequence] biodiversity as a whole.
Reinder Nijland, Wageningen University, Netherlands
Scalable sequencing for environmental research and conservation
From portable yet powerful Flongle and MinION devices to the flexible, high-throughput benchtop GridION and PromethION platforms — scale your sequencing to match your specific environmental sample sequencing requirements.
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MinION
Paired with a contemporary laptop, the MinION is a portable and affordable sequencing device. Perform real-time sequencing at sample source for the fastest access to results. Ideal for in-field or lab-based analysis of eDNA, metabarcoding, and metagenomics.
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Adapting MinION and GridION to run our lowest cost flow cells — ideal for low throughput metabarcoding projects.
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A compact benchtop device offering powerful integrated compute with on-demand access to five independent MinION Flow Cells — run multiple eDNA, metabarcoding, or metagenomics projects on a single device.
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Offering two independent PromethION Flow Cells for low-cost access to high-output sequencing - ideal for smaller sample number whole-genome and transcriptome projects.
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Offering up to 24 or 48 independent, high-capacity flow cells and powerful, integrated compute, PromethION 24 and 48 delivers flexible access to terabases of sequencing data — ideal for high-throughput labs and highly multiplexed samples.
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