The portable MinION is now being used for microbiome analysis in a range of research areas, whether animal gut microbiome analysis or environmental analysis
How is the MinION being used in microbiome research?
- Animal microbiome studies eg mouse gut microbiome
- Metagenomic analysis of complex environmental samples eg Australia’s pink lake, marine microbiomes, urban water samples or from regions of specific environmental interest such as the Arctic or Antarctica.
- Microbiota studies of species taxonomy and relative abundance e.g. WIMP or 16S rRNA, CO1, and ITS
- Many tools are in development to allow real time metagenomic analysis during a MinION run
Real-time data, rapid results
Nanopore sequencing data starts streaming immediately, rather than being delivered in bulk at the end of a 'run'. Real-time data streaming allows immediate analysis of these data, enabling users to determine the presence of markers of antimicrobial resistance more rapidly than with traditional culturing methods. As more data is generated, over time, the user has the ability to generate sufficient data for genome assembly using long reads, which provides the ability to assess whether antimicrobial resistance genes are integrated into the chromosome or present in plasmids. Building on the coverage allows variant detection.Publications related to real-time analysis
How are others using the MinION to address antimicrobial resistance?
|21/07/2017||Using MinION to characterize dog skin microbiota through full-length 16S rRNA gene sequencing approach||BioRxiv|
|17/07/2017||A world of opportunities with nanopore sequencing||PeerJ|
|02/05/2017||Deep Sequencing: Intra-Terrestrial Metagenomics Illustrates The Potential Of Off-Grid Nanopore DNA Sequencing||BioRxiv|
|02/05/2017||Barcode of life: simple laboratory and analysis workflows for 16s and CO1 analysis|
|29/04/2017||Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing||BioRxiv|
|12/01/2017||Evaluation of Oxford Nanopore MinION Sequencing for 16S rRNA Microbiome Characterization||BioRxiv|
|26/11/2016||Complete de novo whole genome assembly made easier with long MinION and PromethION reads|
|04/08/2016||Rapid resistome mapping using nanopore sequencing||Nucleic Acids Research|
|23/07/2016||Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing||Scientific Reports|
What's in my pot (WIMP)
'What's in my pot' (WIMP) is a workflow that enables MinION users to identify bacteria, fungi, viruses or archea in complex samples in real time.
Analysis begins as soon as sequence data starts being streamed (a few seconds after the experiment starts). Each read of streamed sequence data is compared against a database of microbial species, and an identification is made. At the same time, WIMP plots and updates a taxonomic tree of all microorganisms found in the sample.
There are various workflows and techniques that have been developed by members of the nanopore community to perform or enhance assembly and species identification that can be explored in the publications area and within the nanopore community.
How do I get started?
You can start using MinION straight away.
For a $1,000 fee you receive a MinION and starter pack of flow cells and kits. You also get access to a thriving online community of MinION users.