Applications Research areas
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
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)
- 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
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
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.
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)
- 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.
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.
Enhancing microbial genome assemblies
The protozoan parasite Trypanosoma cruzi is the causative agent of Chagas disease (American trypanosomiasis), which affects 6–7 million people worldwide. Due to its highly repetitive genome, current short-read based assemblies are highly fragmented. To enhance functional and comparative studies, researchers in South America utilised nanopore sequencing to generate a more contiguous genome assembly. The facility of long nanopore sequencing reads to span complex genomic regions increased the assembly size by 16 Mb (from 25 Mb to 41 Mb) with 51-fold fewer contigs. Significant increases were also observed in the number of protein coding genes, non-coding genes, and transposable elements.
‘we demonstrate that a single run using the MinION sequencer based on a straightforward 10-min library preparation protocol allows a 67-fold increase in genome contiguity and improves genome completeness by 28%...’Díaz-Viraqué, F. et al. Genome Biol Evol 11(7):1952–1957 (2019).
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.
Automated sample extraction and library preparation — use predefined or custom protocols.View product
Adapting MinION and GridION to run our lowest cost flow cells — ideal for smaller and routine microbial sequencing assays.View product
All the benefits of real-time nanopore sequencing in a pocket-sized, USB-powered device — available from just $1,000, including sequencing reagents.View product
A powerful, portable, and affordable all-in-one sequencing and analysis device. Perform real-time sequencing at sample source for the fastest access to results. Ideal for in-field or lab-based analysis of bacteria, virus, fungi, and small protozoa genomes.View product
Combining up to 24 independent, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of sequencing data — ideal for high-throughput labs and highly multiplexed samples.View products
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.View product