Metagenomic sequencing

Unrestricted nanopore reads deliver enhanced genome assemblies, accurate identification of closely related species, and resolve mobile genetic elements from mixed microbial samples. Real-time data streaming enables immediate access to results, such as species identification, relative abundance, and antimicrobial resistance (AMR) analysis. Combining long reads with targeted approaches enables sequencing of informative genes, such as 16S ribosomal RNA (rRNA) in their entirety, improving resolution of identification.


What is metagenomic sequencing?

Metagenomics is the genomic analysis of multiple organisms from a single sample, revealing insight into the genetic composition of microbial communities. Traditionally, microorganisms have been studied through the culturing of individual species or strains using artificial culture media; however, it has been estimated that less than 2% of bacteria can be cultured in the lab.

Advances in DNA sequencing technologies have enabled the sequencing and analyses of samples containing many species, making it possible to obtain complete or nearly complete genome sequences from uncultured microorganims — providing an important means to study their biology, ecology, and evolution. However, a number of challenges remain, particularly for time-critical or remote sampling applications such as outbreak investigation and pathogen surveillance.

Oxford Nanopore sequencing technology provides a number of key benefits for metagenomics research, including generating reads of unrestricted lengths — from short to ultra-long. Long nanopore reads enhance genome assembly, enabling more accurate analysis of known and novel microbes, and precise differentiation of closely related microbes. Reads exceeding 4 Mb have been achieved with nanopore technology, meaning that entire microbial genomes can be obtained in single reads, or with minimal contigs — uninterrupted stretches of overlapping DNA. Long reads also improve the resolution of repeat sequences and structural variants, further enhancing genome assembly and AMR gene analysis.

Adding a sample to a Flongle Flow Cell on MinION by water

Why nanopore technology for metagenomic sequencing?

Nanopore technology offers a variety of metagenomic approaches — from PCR-free whole-genome sequencing through to amplicon-based 16S rRNA sequencing — that can be used in the lab, field, or limited resource settings.

Using nanopore metagenomic sequencing, you can:

  • Resolve complete genomes and plasmids with reads of unrestricted length
  • Identify species, AMR, and virulence factors in real time
  • Sequence at sample source using portable MinION and Flongle devices
  • Streamline your workflow with 10-minute library preps
  • Detect base modifications and link plasmids to hosts using epigenetic motifs
  • Use intuitive EPI2ME data analysis workflows for real-time species identification and AMR profiling

Get started with metagenomic sequencing

Get best practice recommendations to optimise your end-to-end metagenomic sequencing workflow in our getting started guide.

Experimental approach to metagenomic sequencing

A wide range of library preparation kits are available to suit metagenomic sequencing requirements. Amplification-free kits allow direct sequencing of native DNA, eliminating the potential for PCR bias and enabling the detection of base modifications, such as methylation, alongside the nucleotide sequence without additional sample prep. Amplification-based kits are also available to enable sequencing of the entire 16S rRNA gene, custom regions of interest, or for low sample inputs.

Amplification-free, native DNA sequencing, retaining base modifications Amplification-based sequencing for low input or poor-quality DNA
Ligation Sequencing Kit Rapid Sequencing Kit 16S Barcoding Kit Rapid PCR Barcoding Kit
Preparation time 60 min 10 min 25 min + PCR 15 min + PCR
Input requirement 1,000 ng gDNA; 100–200 fmol amplicons or cDNA 50–100 ng gDNA 10 ng gDNA 1–5 ng gDNA
Fragmentation Optional Transposase-based Not required Transposase-based
Read length Equal to fragment length Equal to fragment length Full-length 16S rRNA gene (~1.5 kb) ~2 kb
Typical output 3/3 2/3 2/3 2/3
Multiplexing options 24 plex, 96 plex 24 plex, 96 plex 24 plex 24 plex
Methylation included Yes Yes - -
Overview Optimised for output, retains base modifications, and enables control over read length. Optimised for simple and rapid library prep, and retains base modifications. Optimised for simple and rapid library prep, and full-length 16S gene sequencing increases taxonomic resolution. Optimised for simple and rapid library prep with low DNA inputs.
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Sequencing devices

Which device for metagenomic sequencing?

From portable, yet powerful Flongle and MinION devices through to the flexible GridION device and high-output PromethION devices — scale your sequencing to match your specific metagenomic sequencing requirements.

Recommended for metagenomic sequencing

PromethION 2 Solo and 2 Integrated

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

Analysis techniques for metagenomic sequencing

Analysis solutions

A range of pipelines and tools are available for the analysis of nanopore metagenomic sequencing data, including workflows that enable bacterial genome assembly, whole-genome and 16S-based taxonomic classification, and AMR profiling. For cloud-based or local analysis, our EPI2ME solutions offer simple, point-and-click workflows via a user-friendly interface for routine metagenomic sample analysis.

Find out more about analysing nanopore metagenomic sequencing data

Featured metagenomic sequencing workflow

For assembly and analysis of microbial genomes from complex metagenomic samples, we recommend the following:

Inspiration for metagenomic sequencing

Discover more about applying metagenomic sequencing to your organism and genomic variants of interest.

Research areas


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