Microbiology & microbial sequencing
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 traditional short-read sequencing technologies. Combining the facility to sequence any length of DNA or RNA fragment — from short to ultra-long (4.2 Mb demonstrated) — with affordable portable and benchtop devices, and real-time results, researchers are now using nanopore technology to fully characterise microbial diversity for a wide range of applications.
Complete and high-quality genome reconstruction
Low entry and sequencing cost facilitates Nanopore sequencing [accessibility] for most research labs, allowing a rapid turnaround time
Liu, L. et al., Microbiome (2022)
Oxford Nanopore sequencing
Traditional short-read technologies
Unrestricted read length (>4 Mb shown)
- Simplify de novo assembly and correct microbial reference genomes using long reads
- Assemble complete genomes and plasmids from metagenomic samples — resolving similar species and complex genomic regions
- Get enhanced taxonomic resolution using full-length reads of informative loci (e.g. entire 16S gene)
- Sequence and quantify full-length transcripts for unambiguous gene expression analysis
- Lack of GC bias allows analysis of a wider range of genomes
Read length typically 50–300 bp
Short sequencing reads may not span complex genomic regions such as repeat elements (e.g. transposons, gene duplications, and prophage sequences), reducing assembly contiguity and potentially missing important genomic information.
Real-time data streaming
- Get immediate access to results, including species identification and AMR profile
- Stop sequencing when sufficient data obtained — wash and reuse flow cell
- Combine with intuitive, real-time EPI2ME data analysis workflows
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 handling large volumes of bulk data.
Sequence anywhere
- Sequence in your lab or in the field with portable Flongle and MinION devices — from just $1,000, including sequencing reagents
- Sequence at sample source, minimise potential sample degradation and eliminate sample shipping delays
- Scale up with high-throughput, modular GridION and PromethION devices
Constrained to the lab
Traditional sequencing technologies are typically expensive, bulky, and require substantial site infrastructure — potentially restricting its usage to well-resourced settings, and delaying time to result.
Direct detection of DNA/RNA methylation
Access methylation data for free (e.g. 5mC, 6mA)
No additional sample prep or sequencing runs required
Train basecalling to identify non-standard base modifications
Separate methylation assay required
Amplification and strand synthesis remove base modification information, necessitating additional upfront sample processing (e.g. bisulfite conversion) and sequencing runs, adding time and expense.
Streamlined workflows
Sample prep in as little as 10 minutes, including multiplexing
Whole genome, metagenomic, targeted (including 16S barcoding), direct RNA, and cDNA sequencing approaches
Eliminate amplification bias with direct, PCR-free protocols
Automated and streamlined sequencing
Laborious workflows
Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency.
Large insights into microorganisms
This White paper explores how microbiologists are now utilising real-time, long-read nanopore sequencing to overcome the challenges associated with traditional short-read sequencing technologies to fully characterise microbial genomes — shedding new light on microbial evolution, pathogenicity, and antimicrobial resistance. Techniques covered include microbial genome assembly, antimicrobial resistance (AMR) profiling, completing plasmid assemblies, investigating virulence, microbial transcriptomics, and the analysis of modified bases.
Access a wealth of microbiology content, including videos, publications, getting started guides, and more in our Resource centre.
Interested in portable sequencing?
Discover how researchers are using MinION for on-site microbial genomics in a wide range of environments, including entirely off-grid sequencing on Europe’s largest ice cap, the crop fields of Africa, and on board the International Space Station.
Find out more in our dedicated portable sequencing resource page.
Generating reference-quality bacterial genome assemblies
Professor Albertson and colleagues, based at Aalborg University in Denmark, investigated whether nanopore sequencing data alone could be used to obtain reference-quality bacterial genome assemblies from sequence data derived from pure cultures/Zymo mock. Find out how they used the latest chemistry to generate near-finished bacterial genomes, without polishing, at a depth of coverage of approximately 40-fold.
Oxford Nanopore R10.4 enables the generation of near-finished microbial genomes from pure cultures or metagenomes at coverages of 40-fold without short-read polishing
Sereika et al. Nature Methods. 19 (2022)
Recovering metagenome-assembled genomes (MAGs) of unculturable bacteria
Nanopore sequencing can be used to sequence unculturable microorganisms directly from extracted DNA samples, enabling the analysis of microorganisms that would be missed by traditional culture-based methods, such as cable bacteria which are long, filamentous bacteria. Discover how Mantas Sereika and his colleagues utilised nanopore sequencing to detect novel genes missing from short-read MAGs to produce the first closed genomes of cable bacteria.
We achieved the first ever closed genomes of cable bacteria … with long-read nanopore sequencing
Mantas Sereika, Aalborg University, Denmark
Scalable sequencing for microbial analysis
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 microbial genomics requirements.
GridION
A compact benchtop device offering powerful integrated compute. Run multiple microbial sequencing and other projects on a single device — from whole genome assembly and targeted sequencing to transcriptomics — using five independent MinION Flow Cells and sample multiplexing.
Combining up to 48 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 48 delivers flexible, on-demand access to terabases of sequencing data.
Flexible, large-scale sequencing using up to 24 independent, high-capacity flow cells.
PromethION 2 devices maintain the flexibility associated with the PromethION 24 and PromethION 48 devices, but in a compact, accessible form factor.
All the benefits of real-time nanopore sequencing in a pocket-sized, USB-powered device.
Adapting MinION and GridION to run our lowest cost flow cells — ideal for smaller or routine assays.
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