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Metagenomic Sequencing (NGS)

Metagenome refers to a collection of total genetic material of a mixed community of organisms, such as environmental metagenome, human metagenome, etc. It contains genomes of both cultivatable and uncultivatable microorganisms. Metagenomic sequencing is a molecular tool used to analyze 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.

Platform:Illumina NovaSeq6000


Service Details

Demo Results

Case Study

Service Advantages

Ø Isolation and cultivation-free for microbial community profiling

Ø High resolution in detecting low-abundance species in environmental samples

Ø The idea of “meta-” integrates all biological features at functional level, species level and gene level, which reflects a dynamic view that is closer to reality.

Ø BMK accumulates massive experience in diverse sample types with over 10,000 samples processed.

Service Specifications

Sequencing Platform

Library

Recommended data yield

Estimated turn-around time

Illumina NovaSeq 6000

PE250

50K/100K/300K Tags

30 Days

Bioinformatics analyses

ü Raw data quality control

ü Metagenome assembly

ü Non-redundant gene set and annotation

ü Species diversity analysis

ü Genetic function diversity analysis

ü Inter-group analysis

ü Association analysis against experimental factors

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Sample Requirements and Delivery

Sample Requirements:

For DNA extracts:

Sample Type

Amount

Concentration

Purity

DNA extracts

> 30 ng

> 1 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

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Sample delivery

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Library construction

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Sequencing

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Data analysis

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After-sale services


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  • 1.Histogram: Species distribution

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    2.Functional genes annotated to KEGG metabolic pathways

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    3.Heat map: Differential functions based on relative gene abundance54.Circos of CARD antibiotic resistance genes

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    BMK Case

    Prevalence of antibiotic resistance genes and bacterial pathogens along the soil-mangrove root continuum

    Published: Journal of Hazardous Materials, 2021

    Sequencing strategy:

    Materials:DNA extracts of four fragments of mangrove root associated samples: unplanted soil, rhizosphere, episphere and endosphere compartments
    Platform: Illumina HiSeq 2500
    Targets: Metagenome
    16S rRNA gene V3-V4 region

    Key results

    Metagenomic sequencing and metabarcoding profiling on soil-root continuum of mangrove saplings were processed in order to study the dissemination of antibiotic resistance genes (ARGs) from soil into plants. Metagenomic data revealed that 91.4% of antibiotic resistance genes were commonly identified in all four soil compartments mentioned above, which shown a continuous fashion. 16S rRNA amplicon sequencing generated 29,285 sequences, representing 346 species. Combining with species profiling by amplicon sequencing, this dissemination was found to be independent of root-associated microbiota, however, it could be facilitated by mobile of genetic elements. This study identified the flow of ARGs and pathogens from soil into the plants through interconnected soil-root continuum.

    Reference

    Wang, C. , Hu, R. , Strong, P. J. , Zhuang, W. , & Shu, L. . (2020). Prevalence of antibiotic resistance genes and bacterial pathogens along the soil–mangrove root continuum. Journal of Hazardous Materials, 408, 124985.

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