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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, closed, and curated genome sequences

Read the paper
Nanopore sequencing provides low-cost long-read data suited to closure of complex genomes including plasmids Baseggio, L. et al. Microb Genom. 7:4 (2021).

Oxford Nanopore sequencing

Traditional short-read technologies

Unrestricted read length (>4 Mb shown)
Enhanced genome assemblies and full-length transcripts

  • 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
Immediate access to microbiology sequence data

  • 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 the lab or at sample source with MinION

  • 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
Analyse microbial methylation as standard

  • 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
Rapid sequencing preparation and results

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. They found that the latest nanopore sequencing chemistries enabled the generation of 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)

Discover more about the benefits of real-time nanopore sequencing for microbial genome assembly, species identification, and gene expression analysis in our applications pages.

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.

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Nanopore sequencing yield chart

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.


Automated sample extraction and library preparation — use predefined or custom protocols.

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Adapting MinION and GridION to run our lowest cost flow cells — ideal for smaller and routine microbial sequencing assays.

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All the benefits of real-time nanopore sequencing in a pocket-sized, USB-powered device — available from just $1,000, including sequencing reagents.

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A powerful, portable, and affordable all-in-one sequencing and analysis device. Ideal for in-field or lab-based analysis of bacteria, virus, fungi, and small protozoa genomes.

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PromethION 2 & 2 Solo

Offering two independent PromethION Flow Cells for low-cost access to high-output sequencing - ideal for smaller sample number whole-genome and transcriptome projects. Available to preorder now.

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PromethION 24

Offering 24 independent, high-capacity flow cells and powerful, integrated compute, PromethION 24 delivers flexible access to terabases of sequencing data — ideal for high-throughput labs and highly multiplexed samples.

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PromethION 48

Our most powerful platform, offering flexible, high-throughput sequencing using up to 48 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation of microbes and their hosts.

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