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)
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 and use in the biopharma sector.
Pathogen surveillance with Oxford Nanopore sequencing
Infectious disease outbreaks have been a threat throughout human history, and driven by factors such as increasing globalisation, population growth, and climate change, that threat is increasing. See how Oxford Nanopore sequencing delivers comprehensive, affordable, portable, and real-time analysis of pathogens.
Related content
Recommended device for microbiology
)
GridION
A compact benchtop device designed to run and analyse up to five MinION Flow Cells. Run multiple microbial sequencing and other projects on a single device — from whole-genome assembly and targeted sequencing to transcriptomics.
Featured analysis for microbiology
)
EPI2ME wf-bacterial-genomes
This workflow enables de novo assembly or alignment of bacterial isolate genomes. It also provides annotation of regions of interest within the assemblies, species identification and sequence typing, and identification of genes and single nucleotide variants associated with antimicrobial resistance.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (50 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 and cell-free DNA (cfDNA)
- Sequence and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- 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)
- Transcript analysis is limited to gene-level expression data
- 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
- 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
