Applications Research areas
Microbiome sequencing & analysis
The study of microbiomes — the genetic material of all microorganisms in a given sample — is providing new insights into a diverse range of research areas, such as human health and disease, crop improvement, and species conservation. Microorganisms and their interactions have a profound effect on their environments, and it is only now, through the advent of modern sequencing technologies, that we are able to fully characterise microbiome samples — not only identifying each individual microbe but also generating complete, closed genome assemblies and elucidating gene expression within microbial communities.
The life and survival of ancient microbial communities
Long reads make it easier to extract original individual genomes from the metagenome Nicole Wagner, Georgetown University, US
Oxford Nanopore sequencing
Traditional short-read technologies
Unrestricted read length (up to 4.2 Mb achieved)
- Generate complete, high-quality metagenome-assembled genomes (MAGs) — resolving closely-related species and complex genomic regions
- Get enhanced taxonomic resolution using full-length reads of informative loci (e.g. entire 16S rRNA gene)
- Sequence and quantify full-length transcripts for unambiguous gene expression and metatranscriptomics studies
Read length typically 50–300 bp
Short sequencing reads may not span complex genomic regions (e.g. repeats, transposons) resulting in fragmented, partial genomes and ambiguous assembly of closely related species. Targeted 16S rRNA sequencing approaches using short reads have also been shown to provide lower taxonomic resolution when compared to long sequencing reads.
In the context of gene expression, the short reads provided by traditional sequencing technology require computational assembly, which has been shown to result in a high proportion of misassembled transcripts, making metatranscriptomics studies highly challenging.
Real-time data streaming
- Identify microorganisms within seconds of starting a sequencing run
- Stop sequencing when sufficient data obtained — wash and reuse flow cell
- Combine with intuitive, real-time EPI2ME data analysis workflows, including metagenomic- and 16S rRNA-based identification and quantification
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
- Characterise microbiomes at their source — minimise potential sample degradation caused by storage or shipping
- Analyse hundreds of samples with flexible, high-throughput, GridION and PromethION devices
Constrained to the lab
Traditional sequencing technologies are typically expensive, bulky, and require substantial site infrastructure — potentially restricting usage to well-resourced settings and delaying time to result.
Direct, amplification-free protocols
- Eliminate amplification- and GC-bias
- Access methylation data for free (e.g. 5mC) — no additional sample prep or sequencing required
- Use methylation motifs to support genome binning and assembly from metagenome samples — maximising the utility of your data
Separate methylation assay required
Amplification can introduce bias — reducing uniformity of coverage with the potential for coverage gaps — and removes base modifications (e.g. DNA methylation) limiting data insights.
Streamlined workflows
- Sample prep in as little as 10 minutes, including multiplexing
- Whole genome, metagenomic, targeted (including 16S rRNA), direct RNA, and cDNA sequencing approaches
- Automate sample prep using the portable VolTRAX device
Laborious workflows
Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency.
White paper
Addressing the challenges of metagenomics
Understanding the true diversity and interactions of microorganisms in any given environment has historically been restricted by many factors, including the inability to culture the vast majority of microbes on artificial media. Developments in traditional sequencing technologies removed the need for culture, providing more detailed insights into microbiomes; however, many challenges remained, including the assembly of complete genomes, distinguishing closely related species, time to result, and sequencing infrastructure. This White paper reviews how nanopore sequencing is being used by researchers worldwide to meet these challenges, shedding new light on the composition and function of microbiomes — from the human gut to the most remote environments on Earth and beyond.
Access a wealth of microbiome sequencing and analysis content, including videos, publications, small genome and metagenomic sequencing 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
Complete, closed bacterial genomes from the human gut microbiome
It is estimated that the human body contains as many microbes (30 trillion) as it does human cells; the composition of these microbes can profoundly influence human health and disease. Hear how Dr. Ami Bhatt and colleagues at Stanford University, USA, are using long nanopore sequencing reads to explore how changes in the human gut microbiome affect treatment outcomes of immunocompromised individuals.
‘[this method] represents an effective, straightforward solution for the complete and efficient de novo characterization of structurally complex bacterial genomes within the gut microbiome’
Ami Bhatt, Stanford University, USA
Discover more about the benefits of long reads and real-time nanopore sequencing for whole genome assembly, species identification, and gene expression analysis in our applications pages.
Get started
Scalable sequencing for microbiome 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 microbiome analysis requirements.
Recommended for microbiome sequencing
MinION Mk1C
A powerful, portable, and affordable all-in-one sequencing and analysis device. Analyse microbiomes in real time, in the lab or at sample source, for the fastest access to results.
VolTRAX
Automated sample extraction and library preparation — use predefined or custom protocols.
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Flongle
Adapting MinION and GridION to run our lowest cost flow cells — ideal single microbiome samples or routine analysis of microbial swabs.
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MinION
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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GridION
A compact benchtop device offering powerful integrated compute. Run multiple microbiome and other sequencing projects on a single device using five independent MinION Flow Cells and sample multiplexing.
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PromethION 24
Combining up to 24 individual, 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.
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PromethION 24
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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