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.

Low entry and sequencing cost facilitates Nanopore sequencing [accessibility] for most research labs, allowing a rapid turnaround time

Liu, L. et al., Microbiome (2022)

Technology comparison

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

Laborious workflows

Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency.

White paper

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.

Case study

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)

Case study

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

Get started

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.

Recommended for microbiology


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.


Get in touch

Talk to us

If you have any questions about our products or services, chat directly with a member of our sales team.

Book a sales call

To book a call with one of our sales team, please click below.