Microbiome sequencing
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
Generate complete, reference-quality metagenome-assembled genomes (MAGs) with long, accurate nanopore reads
Sequence at source, even in the most extreme environments with the portable MinION
Identify microorganisms immediately during a sequencing run with real-time data streaming
Simplify genome assembly
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, food safety, and species conservation. Microorganisms and their interactions have a profound effect on their environments, and it is only now, through the advent of nanopore 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.
)
Featured content
)
Metagenomic assembly using long reads
Metagenomic sequencing with nanopore technology allows the rapid identification and analysis of culturable and unculturable microorganisms. This workflow outlines a simple method for sequencing and assembling microbial genomes from metagenomic samples.
)
Microbial sequencing with Oxford Nanopore
High-accuracy nanopore sequencing overcomes the limitations of legacy technology to characterise complete, contiguous, high-quality microbial genomes. This guide provides a complete introduction to microbial sequencing using nanopore technology.
Related content
)
)
)
)
PromethION 2 devices
Offering flexible, affordable, high-output nanopore devices for every lab in a compact, accessible form. Ideal for obtaining complete, circular MAGs from complex microbial samples in real time.
)
Adapting MinION and GridION devices to enable direct, real-time DNA sequencing, or cDNA sequencing, on smaller, single-use flow cells.
)
The only portable, real-time devices for DNA and RNA sequencing, giving complete control and creativity over when, where, and how often you sequence, regardless of application.
)
A compact benchtop device designed to run and analyse up to five Flongle or MinION Flow Cells.
)
Flexible, large-scale, direct DNA and RNA sequencing devices — delivering on-demand access to terabases of data.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (20 bp to >4 Mb)
Short read length (<300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Perform cost-effective targeted analyses with single-use Flongle Flow Cells
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
