Metagenomic Sequencing-Nanopore
Service Advantages
● High-quality assembly-Enhancing accuracy of species identification and funcational gene prediction
● Closed bacterial genome isolation
● More powerful and reliable application in diverse area, e.g. detection of pathogenic microorganisms or antibiotic resistance related genes
● Comparative metagenome analysis
Service Specifications
|
Platform |
Sequencing |
Recommended data |
Turnaround Time |
|
Nanopore |
ONT |
6 G/10 G |
65 Working days |
Bioinformatics analyses
● Raw data quality control
● Metagenome assembly
● Non-redundant gene set and annotation
● Species diversity analysis
● Genetic function diversity analysis
● Inter-group analysis
● Association analysis against experimental factors
Sample Requirements and Delivery
Sample requirements and delivery
Sample Requirements:
For DNA extracts:
|
Sample Type |
Amount |
Concentration |
Purity |
|
DNA extracts |
＞ 4 μg |
＞ 20 ng/μl |
OD260/280= 1.6-2.5 |
For environmental samples:
|
Sample type |
Recommended sampling procedure |
|
Soil |
Sampling amount: approx. 5 g; Remaining withered substance needs to be removed from surface; Grind large pieces and pass through 2 mm filter; Aliquot samples in sterile EP-tube or cyrotube for reservation. |
|
Feces |
Sampling amount: approx. 5 g; Collect and aliquot samples in sterile EP-tube or cryotube for reservation. |
|
Intestinal contents |
Samples need to be processed under aseptic condition. Wash collected tissue with PBS; Centrifuge the PBS and collect the precipitant in EP-tubes. |
|
Sludge |
Sampling amount: approx. 5 g; Collect and aliquot sludge sample in sterile EP-tube or cryotube for reservation |
|
Waterbody |
For sample with limited amount of microbial, such as tap water, well water, etc., Collect at least 1 L water and pass through 0.22 μm filter to enrich microbial on the membrane. Store the membrane in sterile tube. |
|
Skin |
Carefully scrape skin surface with sterile cotton swab or surgical blade and place it in sterile tube. |
Recommended Sample Delivery
Freeze the samples in liquid nitrogen for 3-4 hours and store in liquid nitrogen or -80 degree to long-term reservation. Sample shipping with dry-ice is required.
Service Work Flow
Sample delivery
Library construction
Sequencing
Data analysis
After-sale services
1.Heatmap: Species richness clustering
2.Functional genes annotated to KEGG metabolic pathways
3.Species correlation network
4.Circos of CARD antibiotic resistance genes
BMK Case
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
Published: Nature Biotechnology, 2019
Technical Highlights
Sequencing: Nanopore MinION
Clinical metagenomics bioinformatics: Host DNA depletion, WIMP and ARMA analysis
Rapid detection: 6 hours
High sensitivity: 96.6%
Key results
In 2006, lower respiratory infection(LR) caused 3 million human death globally. The typical method for LR1 pathogen detection is cultivation, which has poor sensitivity, long turn-around-time and is lack of guidance in early antibiotic therapy. A rapid and accurate microbial diagnosis has long been an urgent need. Dr. Justin from University of East Anglia and his partners successfully developed a Nanopore-based metagenomic method for pathogen detection. According to their workflow, 99.99% of host DNA can be depleted. Detection in pathogens and antibiotic resistant genes can be finished in 6 hours.
Reference
Charalampous, T. , Kay, G. L. , Richardson, H. , Aydin, A. , & O’Grady, J. . (2019). Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nature Biotechnology, 37(7), 1.
