Microbial genetics
... our results demonstrate that [Oxford Nanopore Technologies] can be used as a cost-effective sequencing strategy, without the need for complementing with other sequencing technologies, for the reconstruction of complete genomes of the highest quality
Soto-Serrano et al. bioRxiv (2024)
Assemble complete genomes and plasmids from metagenomic samples — resolving closely related species
Scale your sequencing to your needs — run one to thousands of samples on a single device
Span entire SVs and repeat-rich regions — characteristic of AMR genes — in long nanopore reads
Fully characterise microbial genomes
Microorganisms are the most abundant and diverse forms of life on Earth, with estimates ranging from millions to trillions of species; however, only a small percentage have been identified, let alone sequenced. Of the ~400,000 microbial strains for which sequencing data is available, the majority of genomes are incomplete, reflecting the inherent challenges associated with legacy short-read sequencing technologies. Combining the ability to sequence any length of DNA or RNA fragment — from short to ultra-long (4.2 Mb achieved) — with affordable portable and benchtop devices and real-time results, researchers are using scalable nanopore technology to fully characterise microbial diversity for a wide range of applications.
)
Featured content
)
Bacterial isolate sequencing
The nanopore-only microbial isolate sequencing solution (NO-MISS) is an end-to-end workflow providing a flexible and rapid approach for whole-genome sequencing of bacterial isolates, generating data for a range of applications from public health to clinical microbiology research.
)
Large insights into microorganisms
Over 490,000 microbial strains have been sequenced, but approximately 90% of bacterial genomes are thought to be incomplete. Find out how nanopore sequencing is being utilised by researchers to fully characterise microbial genomes.
Related content
)
)
)
GridION
A compact benchtop device designed to run and analyse up to five Flongle or MinION Flow Cells. Run multiple microbial sequencing and other projects on a single device — from whole-genome assembly and targeted sequencing to transcriptomics.
)
Adapting MinION and GridION devices to enable direct, real-time DNA sequencing, or cDNA sequencing, on smaller, single-use flow cells.
)
The only portable, real-time devices for DNA and RNA sequencing, giving complete control and creativity over when, where, and how often you sequence, regardless of application.
)
Flexible, affordable, high-output nanopore devices for every lab — in a compact, accessible form.
)
Flexible, large-scale, direct DNA and RNA sequencing devices — delivering on-demand access to terabases of data.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (20 bp to >4 Mb)
Short read length (<300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Perform cost-effective targeted analyses with single-use Flongle Flow Cells
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
