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.

This is a great example of where Nanopore sequencing really opened up a new window into a biological entity that we really didn’t know existed before we applied this tech

Ed DeLong, University of Hawai’i at Mānoa, USA

Technology comparison

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 detection of DNA/RNA methylation

  • Eliminate amplification- and GC-bias

  • Access methylation data for free (e.g. 5mC, 6mA) — 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

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

Characterising the complex microbial communities of permafrost

Permafrost is defined as an area that has remained continuously frozen for at least two consecutive years, but permafrost-covered regions in most cases have remained frozen for hundreds or thousands of years. With nanopore technology, rapid and thorough characterisation of the microbial communities can be achieved, including the complex regions that are typically difficult to sequence with short-read techniques. Find out how Devin Drown and his team have utilised long nanopore reads to see how the thawing of permafrost is affecting soil microbial communities.

Case study

Using nanopore sequencing in a food microbiology laboratory

Microbiome sequencing has multiple potential applications in a food microbiology laboratory, including pathogen characterisation and food spoilage investigation. Long nanopore reads can be used for rapid microbial identification, including for samples that cannot be confirmed with traditional cultural methods. Find out how Andrzej Benkowski and his colleagues use efficient nanopore sequencing workflows for bacterial and metagenomic identification in food samples, with rapid turnaround times.

The use of the ONT long read sequencing is a powerful tool that can be utilised in a high throughput [microbiology] lab due to its ease of use, price competitiveness, reliable data and rapid time to result using basic ONT workflow and EPI2ME bioinformatics.

Andrzej Benkowski, Eurofins, USA

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

PromethION 2 Solo & 2 Integrated

Offering two independent PromethION Flow Cells for cost-efficient access to high-output sequencing ─ ideal for obtaining complete circular genomes from complex metagenomics samples.


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.