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Metagenomic Sequencing-Nanopore

Metagenomics is a molecular tool used to analyse the mixed genomic materials extracted from environmental samples, which provides detailed information in species diversity and abundancy, population structure, phylogenetic relationship, functional genes and correlation network with environmental factors, etc. Nanopore sequencing platforms has recently introduced to metagenomic studies. Its outstanding performance in read length largely enhanced down stream metagenomic analysis, especially metagenome assembly. Taking advantages of read-length, Nanopore-based metagenomic study is able to achieve more continuous assembly comparing with shot-gun metagenomics. It has been published that Nanopore-based metagenomics successfully generated complete and closed bacterial genomes from microbiomes (Moss, E. L., et. al, Nature Biotech, 2020)

Platform:Nanopore PromethION P48

Service Details

Demo Results

BMK Case

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



Recommended data 

Turnaround Time



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




DNA extracts

1-1.5 μg

> 20 ng/μl

OD260/280= 1.6-2.5

For environmental samples:

Sample type

Recommended sampling procedure


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.


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.


Sampling amount: approx. 5 g; Collect and aliquot sludge sample in sterile EP-tube or cryotube for reservation


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.


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

Sample delivery

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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  • 1.Heatmap: Species richness clustering32.Functional genes annotated to KEGG metabolic pathways43.Species correlation network54.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.

    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.

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