The identification of microbial species has depended predominantly upon culture-based techniques. However, the difficulty with which types of organisms are cultured implies that the grown species may be overrepresented by both cultivation and plate counts.
Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques.
With its small size and low cost, the hand-held MinION sequencer is a powerful tool for in-field surveillance. Using a metagenomic approach, it allows non-targeted detection of viruses in a sample within a few hours.
The Oxford Nanopore MinION sequencing platform offers direct analysis of DNA reads as they are generated, which combined with its low cost, low power and extremely compact size, makes the device attractive for in-field or clinical deployment, e.g. rapid diagnostics.
Genetic and genomic analysis of nucleic acids from environmental samples has helped transform our perception of the subsurface as a major reservoir of microbial novelty. Many of the microbial taxa living in the subsurface are under-represented in culture-dependent investigations.
The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics.
Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted because of fixed-time sequencing runs and cumbersome bioinformatics workflows.
Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing is now feasible, but has been limited to date by concerns regarding sensitivity and sample-to-answer turnaround times.
The Applications team at Oxford Nanopore has two overarching responsibilities: creation and development of sample and library preparation protocols for a wide variety of sample types, and undertaking biological projects which highlight the various strengths of Oxford Nanopore’s technology.
Background: The miniaturised and portable DNA sequencer MinION has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches.
Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionise genomics. Several applications, including RNA-seq, haplotype sequencing and 16S sequencing, are however limited by its relatively high single read error rate (>10%).