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16S/18S/ITS Amplicon Sequencing-NGS

Amplicon sequencing with Illumina technology, specifically targeting the 16S, 18S, and ITS genetic markers, is a powerful method for unraveling the phylogeny, taxonomy, and species abundance within microbial communities. This approach involves sequencing the hypervariable regions of housekeeping genetic markers. Originally introduced as a molecular fingerprint by Woeses et al in 1977, this technique has revolutionized microbiome profiling by enabling isolation-free analyses. Through the sequencing of 16S (bacteria), 18S (fungi), and Internal Transcribed Spacer (ITS, fungi), researchers can identify not only abundant species but also rare and unidentified ones. Widely adopted as a pivotal tool, amplicon sequencing has become instrumental in discerning differential microbial compositions across diverse environments, including the human mouth, intestines, stool, and beyond.

Service Details


Demo Results

Featured publications

Service Features

●  Sequencing platform: Illumina NovaSeq.

●  Amplification of short regions of 16S, 18S and ITS, among other amplification targets.

●  Flexible choices of amplicon.

●  Previous project experience with multiple amplification targets.

Service Advantages

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

●  High resolution: in low-abundant components in environmental samples.

●  Widely applicable: to diverse microbial community studies.

●  Comprehensive bioinformatic analysis: including the with latest QIIME2 package (quantitative insight into microbial ecology) with diverse analyses in terms of database, annotation, OTU/ASV.

●  Extensive Expertise: with thousands of amplicon sequencing projects conducted annually, BMKGENE brings over a decade of experience, a highly skilled analysis team, comprehensive content, and excellent post-sales support.

Service Specifications


Sequencing Strategy

Data recommended

Quality control


Illumina PE250

50/100K tags (read pairs)


Service Requirements

Concentration (ng/µL)

Total amount (ng)

Volume (µL)






● Soil/sludge: 1-2g
● Intestinal content-animal: 0.5-2g
● Intestinal contents-insect: 0.1-0.25g
● Plant surface (enriched sediment): 0.1-0.5g
● Fermentation broth enriched sediment): 0.1-0.5g
● Faeces (large animals): 0.5-2g
● Faeces (mouse): 3-5grains
● Pulmonary alveolar lavage fluid: filter paper
● Vaginal swab: 5-6 swabs
● Skin/genital swab/saliva/oral soft tissue/pharyngeal swab/rectal swab: 2-3 swabs
● Surface microorganisms: filter paper
● Waterbody/air/biofilm: filter paper
● Endophytes: 1-2g
● Dental Plaque: 0.5-1g

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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    Includes the following analysis:

    • Raw data quality control
    • OTU clustering /De-noise(ASV)
    • OTU annotation
    • Alpha diversity analysis: multiple indexes, including Shannon, Simpson and ACE.
    • Beta diversity analysis
    • Inter-group analysis
    • Correlation analysis: between environmental factors and OUT composition and diversity
    • 16S functional gene prediction

    Histogram of taxonomic distribution




    taxonomic abundance clustering heat map



    Alpha diversity analysis: rarefaction curve



     beta diversity analysis: NMDS



    Intergroup analysis: LEFSE biomarker discovery





    Explore the advancements facilitated by BMKGene’s amplicon sequencing services with Illumina through a curated collection of publications.

    Dong, C. et al. (2022) ‘Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides’, Frontiers in Microbiology, 13. doi: 10.3389/FMICB.2022.855317/FULL.

    Li, Y. et al. (2023) ‘Synthetic bacterial consortia transplantation for the treatment of Gardnerella vaginalis-induced bacterial vaginosis in mice’, Microbiome, 11(1), pp. 1–14. doi: 10.1186/s40168-023-01497-y

    Yang, J., Fu, Y. and Liu, H. (2022) ‘Microbiomes of air dust collected during the ground-based closed bioregenerative life support experiment “Lunar Palace 365”’, Environmental Microbiomes, 17(1), pp. 1–20. doi: 10.1186/S40793-022-00399-0/FIGURES/8.

    Yin, S. et al. (2022) ‘Feedstock-dependent abundance of functional genes related to nitrogen transformation controlled nitrogen loss in composting’, Bioresource Technology, 361, p. 127678. doi: 10.1016/J.BIORTECH.2022.127678.

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