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16S/18S/ITS Amplicon Sequencing-NGS

16S/18S/ITS amplicon sequencing aims at revealing phylogeny, taxonomy, and species abundance in a microbial community by investigating PCR products of housekeeping genetic markers that contain both highly conversed and hypervariable parts. The introduction of these perfect molecular fingerprint by Woeses et al,(1977) empowers  isolation-free microbiome profiling. Sequencing of 16S (bacteria), 18S (fungi) and Internal transcribed spacer(ITS, fungi) allows identification of both abundant species as well as rare and unidentified species. This technology has becoming a widely applied and major tool in identifying differential microbial composition in various environments, such as human mouth, intestines, feces, etc.

Platform:Illumina NovaSeq6000 

Service Details

Demo Results

Case Study

Service Advantages

● Isolation-free and rapid identification of microbial composition in environmental samples

● High resolution in low-abundant components in environmental samples

● Latest QIIME2 analyzing flow with diverse analyses in terms of database, annotation, OTU/ASV.

● High-throughput, higher accuracy

● Applicable to diverse microbial community studies

● BMK owns extensive experience with over 100,000 samples/year,covering soil, water, gas, sludge, feces, intestines, skin, fermentation broth, insects, plants, etc.

● BMKCloud facilitated data interpretation containing 45 personalized analyzing tools

Service Specifications

Sequencing Platform


Recommended data yield

Estimated turn-around time

Illumina NovaSeq 6000


50K/100K/300K Tags

30 Days

Bioinformatics analyses

● Raw data quality control

● OTU clustering/De-noise(ASV)

● OTU annotation

● Alpha diversity

● Beta diversity

● Inter-group analysis

● Association analysis against experimental factors

● Function gene prediction


Sample Requirements and Delivery

Sample Requirements:

For DNA extracts:

Sample Type




DNA extracts

> 30 ng

> 1 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.Species distribution 


    2.Heat map: Species richness clustering


    3.Rare faction curve


    4.NMDS analysis


    5.Lefse analysis





    BMK Case

    Obese Individuals with and without Type 2 Diabetes show different gut microbial  functional capacity and composition

    Published: Cell Host & Microbe, 2019

    Sequencing strategy:

    Lean non-diabetes (n=633); Obese non-diabetes (n=494); Obese-Type 2 diabetes (n=153);
    Target region: 16S rDNA V1-V2
    Platform: Illumina Miseq (NGS-based amplicon sequencing)
    Subset of DNA extracts were subjected to metagenomic sequencing on Illumina Hiseq

    Key results

    Microbial profilings of these metabolic diseases were successfully differentiated.
    By comparing microbial features generated by 16S sequencing, obesity was found to associated with changes in microbial composition, individual features, especially significant decrease in Akkermansia, Faecalibacterium, Oscillibacter, Alistipes, etc. In addtion, T2D was found associated with increase in Escherichia/shigella.


    Thingholm, L. B. , et al. “Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.” Cell Host & Microbe 26.2(2019).


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