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Metagenomics and microbiome analysis with nanopore technology

Long nanopore sequencing reads deliver enhanced genome assemblies, accurate identification of closely related species, and unambiguous analysis of full-length RNA transcripts from mixed microbial samples. Data is provided in real-time, enabling immediate access to results such as species identification, abundance, and antimicrobial resistance. Combining long reads with targeted approaches enables sequencing of informative genes (e.g. 16S rRNA) in their entirety, improving resolution of identification.

  • Assemble complete genomes and plasmids from mixed metagenomic samples
  • Identify microbes and antimicrobial resistance (AMR) in real-time and differentiate closely related strains using long reads
  • Streamline your workflow with rapid whole genome or targeted (e.g. 16S rDNA) approaches — multiplex samples for even more cost-efficient results
  • Sequence at sample source using portable MinION and Flongle devices — get started from just $1,000
  • Simplify metatranscriptomics studies using full-length transcripts
  • Eliminate PCR bias, identify base modifications, and link plasmids to hosts using direct sequencing

How will you use nanopore technology?

Whole genome metagenomics

Targeted metagenomics



Long-read nanopore sequencing technology improves on the traditional gene-level shotgun metagenomic analysis provided by short-read sequencing approaches to enable unbiased assembly of complete, closed genomes and plasmids from clinical research and microbiome samples. Discriminate closely related species, resolve challenging repeat regions and structural variants, and delineate plasmid and genomic AMR genes. Data is delivered in real time, providing rapid sample insights.

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

Improve the precision of targeted metagenomic species identification using long sequencing reads. By enabling the sequencing of complete genes (e.g. 16S rRNA) and/or operons — including repetitive regions – long nanopore sequencing reads have been shown to offer more comprehensive identification of species in mixed microbial communities. Eliminate upstream targeted assay prep using adaptive sampling — real-time, on-device enrichment of sequences of interest. 

  • Analyse entire genes or operons to enhance precision of species identification
  • Eliminate upfront, lab-based sequence enrichment using adaptive sampling 
  • Sequence samples at source using the portable MinION or Flongle
  • Go from sample to result in <40 minutes using the 16S Rapid Sequencing Kit
  • Identify species and abundance in real-time using intuitive EPI2ME data analysis workflows
  • Multiplex samples for even more cost-effective results
  • Automate sample prep using the portable VolTRAX device

The long reads provided by nanopore technology enable sequencing of full-length transcripts in single reads, precluding the requirement for complex and often inaccurate post-sequencing transcript assembly. The unambiguous identification of transcript isoforms significantly simplifies the study of gene expression in mixed microbial communities and provides an alternative method of identifying pathogens from metagenomic samples.

  • More easily assign transcripts to species using full-length reads
  • No requirement for complex transcript assembly
  • High yields enable accurate transcript quantification
  • Eliminate PCR bias using direct cDNA or direct RNA sequencing
  • Get higher yields from less input using the latest RNA and cDNA sequencing kits
  • Retain and analyse base modifications (e.g. methylation) using direct RNA sequencing

Use direct nanopore sequencing reads to determine the epigenetic profile of individual organisms from mixed microbial communities. Utilise epigenetic information to further enhance the precision of species identification and link mobile genetic elements such as plasmids to their host organisms. 

  • Identify modified bases and nucleotide sequence in a single assay
  • Discriminate base modifications from closely related species using long reads
  • Utilise base modifications to enhance species identification 
  • Match mobile genetic elements to host organisms using epigenetic motifs
  • Streamline your workflow — 10-minute library prep (DNA) with no bisulfite or chemical conversion required
  • Capture base modifications as standard — analyse when you are ready

'we demonstrated in the microbiome analysis the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes, and for the first time, identifying misassembled metagenomic contigs'

Tourancheau et al

Discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiome using nanopore sequencing