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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

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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) High-quality MAGs and transcriptomes with long reads

  • 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 Rapid, real-time microbiome analysis

  • 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 Portable microbiome analysis with MinION

  • 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 Study the impact of methylation on microbiomes

  • 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 Simple and fast sample prep

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

High-quality, low-cost, nanopore-only bacterial genome sequences

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 activated sludge. Traditionally, researchers used either short-read or reference polishing of nanopore data, yet this is undesirable as it adds cost and complexity. The team introduced the term ‘near-finished’ genome to indicate the generation of a high-quality genome assembled with only long nanopore reads, for which the application of short-read polishing would not significantly improve the consensus sequence. They found that the latest nanopore sequencing chemistries enabled the generation of near-finished bacterial genomes from activated sludge samples, without polishing.

‘We show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing’

Sereika et al. Nature Methods. 19 (2022)

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.

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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.

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Output of sequencing devices

Recommended for microbiome sequencing

PromethION 2 & 2 Solo

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


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 single microbiome samples or routine analysis of microbial swabs.

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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. Analyse microbiomes in real time, in the lab or at sample source, for the fastest access to results.

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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

With up to 24 individual, 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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