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16S/18S/ITS Amplicon Sequencing-PacBio

The subunit on 16S and 18S rRNA containing both highly conserved and hyper-variable regions is a perfect molecular fingerprint for prokaryotic and eukaryotic organisms identification. Taking advantage of sequencing, these amplicons can be targeted based on the conserved parts and the hyper-variable regions can be fully characterized for microbial identification contributing to studies covering microbial diversity analysis, taxonomy, phylogeny, etc. Single-molecule real-time(SMRT) sequencing of PacBio platform enables obtaining of highly accurate long reads, which could cover full-length amplicons (approx. 1.5 Kb). The widen view of genetic field greatly enhanced the resolution in species annotation in bacteria or fungi community.

Platform:PacBio Sequel II 

Service Details

Demo Results

Case Study

Service Advantages


● Long-reads revealing full-length sequence of 16S/18S/ITS

● Highly accurate base calling with PacBio CCS mode sequencing

● Species-level resolution in OTU/ASV annotation

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

● 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 

 Turnaround Time

PacBio Sequel II


5K/10K/20K Tags

44 Working 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

> 1 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.Annotation rate of V3+V4(Illumina)-based microbial community profiling vs. Full-length (PacBio)-based profiling.
    (Data of 30 randomly picked projects were applied for statistics)


    2.Annotation rate of full-length amplicon sequencing at species-level in different sample types


    3.Species distribution

    4.Phylogenetic tree


    BMK Case

    Arsenic exposure induces intestinal barrier damage and consequent activation of gut-liver axis leading to inflammation and pyroptosis of liver in ducks

    Published: Science of the Total Environment, 2021

    Sequencing strategy:

    Samples: Control vs 8 mg/kg ATO exposed group
    Sequencing data yield: 102,583 raw CCS sequences in total
    Control: 54,518 ± 747 effective CCS
    ATO-exposed : 45,050 ± 1675 effective CCS

    Key results

    Alpha diversity: ATO exposure significantly altered the intestinal microbial richness and diversity in the ducks.

    Metastats analysis:
    In phylum level: 2 bacterial phyla only detected in control groups
    In genus level: 6 genera were found significantly different in relative abundance
    In species level: 36 species were identified in total, with 6 of them significantly different in relavive abundance


    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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