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.

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

Technology comparison

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

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.

White papers

Addressing the challenges of metagenomics with nanopore sequencing

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.

Get more environmental sequencing resources, 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).

Case study

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

Case study

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

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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.

Recommended for environmental genomics


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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