Environmental research and conservation
Portable, affordable nanopore sequencing technology delivers unique opportunities for environmental research and 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 sequencing reads provide enhanced species identification, while real-time data analysis delivers immediate access to results, whether in the field or in the lab.
Oxford Nanopore sequencing
Traditional short-read technologies
Sequence at sample source or lab
- Powerful, portable devices — starting at just $1,000, including sequencing reagents
- Get faster access to results — no more sample shipping delays
- Minimise potential for sample degradation — reveal the true biology
Constrained to the lab
Traditional sequencing technologies are typically bulky, cumbersome to ship, and require substantial site infrastructure, making them difficult to deploy in mobile settings or remote locations — where much of the world’s biodiversity is located.
Real-time data streaming
- Analyse data as it is generated for rapid insights
- Stop sequencing when sufficient data obtained — wash and reuse flow cell
- Use intuitive EPI2ME workflows for real-time microbiome analysis
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 shown)
- Get enhanced phylogenetic and taxonomic resolution through metabarcoding with full-length reads of informative loci (e.g. entire 16S and CO1 genes)
- Assemble complete genomes and plasmids from metagenomic samples — resolving similar species and complex genomic regions
Read length typically 50–300 bp
Short sequencing reads may not 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.
Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency. Base modifications (e.g. methylation) are not detected as standard, with extra preparation steps and additional sequencing runs required.
Addressing the challenges of metagenomics
Microbial communities can have a profound effect on their environment, for example breaking down pollutants 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, which interrogates the genetic material of all microorganisms in a given community, not only provides significant insights into the structure and function of microbial communities but can also 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.
Get more environmental sequencing content, including eDNA, metabarcoding, and metagenomics publications, posters, and videos, in our Resource centre, or visit our Portable sequencing page.
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.
ORG.one supports the sequencing of species from the IUCN Red List, specifically the critically endangered and extinct in the wild categories (more than 8000 species)
Metagenomic analysis of microbial communities in permafrost thaw
Taking advantage of the long sequencing reads generated by nanopore technology, Devin Drown and his team at the University of Alaska Fairbanks, USA, have been researching how the thawing of permafrost may affect soil microbial communities. Devin and his team chose nanopore technology for a rapid and thorough characterisation of the complex microbial communities in the active layers. Long, PCR-free nanopore sequencing reads enable access to regions that are difficult to sequence with traditional short-read sequencing technologies, facilitating the assembly of accurate microbial genomes from complex communities.
ORG.one: a new program to promote sequencing biodiversity
As part of the ORG.one initiative to support faster, more localised sequencing of critically endangered species, Tomas Marques-Bonet and his team at the Institute of Evolutionary Biology in Spain are sequencing nine species (covering birds, mammals, and amphibians) to develop improved genome assemblies to support conservation efforts. Using nanopore sequencing, high-quality genome assemblies for all species were generated within approximately two months. Read N50s ranged between 20-40 kb, with contig N50s of 30-50 Mb, which according to Tomas is 'quite remarkable'. The team are now performing population genomics studies to better understand conservation status. The data generated is online and open access to encourage further scientific and community support for this vital initiative.
Using nanopore sequencing to monitor circulation of SARS-CoV-2 in wastewater
Wastewater surveillance of SARS-CoV-2 has acted as a complementary approach to clinical surveillance to monitor levels of the virus in wastewater as an early warning indicator of increasing community infections. At the NCM 2022, Samuel Fisch (Tulane University School of Public Health and Tropical Medicine, USA) explained how he used nanopore sequencing of wastewater for surveillance of SARS-CoV-2 levels in sewers from the Michigan State University campus. The results demonstrate that wastewater sequencing can be used as a rapid, real-time, cost-effective public health tool for detecting emerging SARS-CoV-2 variants.
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.
* Theoretical max output (TMO). Assumes system is run for 72 hours (or 16 hours for Flongle) at 420 bases / second. Actual output varies according to library type, run conditions, etc. TMO noted may not be available for all applications or all chemistries.
A powerful, portable, and affordable all-in-one sequencing and analysis 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.
Portable, USB-powered, automated sample extraction and library preparation — use predefined or custom protocols.
Adapting MinION and GridION to run our lowest cost flow cells — ideal for low throughput metabarcoding projects.
All the benefits of real-time nanopore sequencing in a pocket-sized, USB-powered device — available from just $1,000, including sequencing reagents.
A compact benchtop device offering powerful integrated compute with on-demand access to 5 independent MinION Flow Cells — run multiple eDNA, metabarcoding, or metagenomics projects on a single device.
Offering two independent PromethION Flow Cells for low-cost access to high-output sequencing - ideal for smaller sample number whole-genome and transcriptome projects. Available to preorder now.
Offering 24 independent, high-capacity flow cells and powerful, integrated compute, PromethION 24 delivers flexible access to terabases of sequencing data — ideal for high-throughput labs and highly multiplexed samples.
Our most powerful platform, offering flexible, high-throughput sequencing using up to 48 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation of large sample numbers.
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