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Nanopore-Based 16S/18S/ITS Sequencing

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A direct PCR approach is applied to our nanopore-based full-length 16S/18S/ITS sequencing, allowing the direct amplification of 16S/18S/ITS sequences from bacterial/archaeal/fungal/eukaryotic cell suspensions via PCR without DNA purification. This approach overcomes the limitations of the traditional culture-based bacterial identification, instead providing rapid and accurate microbial identification and diversity analysis.

Our Advantages:
  • Rapid and easy streamlining workflow to identify bacteria and archaeal at the species level.
  • Multiplexing sequencing enables more cost-effective and rapid results.
  • Long reads enable more efficient analysis and removal of potential sources of bias.
Tell Us About Your Project

We are dedicated to providing outstanding customer service and being reachable at all times.

Request a Quote

Nanopore-based 16S/18S/ITS sequencing platform

The 16S rRNA gene is present in all archaea and bacteria, and consists of conserved and highly variable regions, making it ideal for the identification of prokaryotes. The 18S rRNA gene and internally transcribed spacer (ITS) are present in all eukaryotes and are suitable for eukaryotic identification and diversity analysis. Nanopore sequencing, a long-read sequencing technology, has obvious advantages in generating a more accurate profile of the microbiome than short-read sequencing technologies. It holds the promise of a microbiology revolution through generating real-time, long reads, with continuously increasing accuracy. Our nanopore-based 16S/18S/ITS sequencing provides rapid and accurate prokaryotic identification analysis with a relatively simple workflow and no need for DNA purification.

Nanopore-based 16S/18S/ITS sequencing is a novel molecular approach, with a more comprehensive and rapid process compared to the traditional culture-based bacterial identification,  for the taxonomic characterization of microbial communities. In microbiology, nanopore-based full-length 16S/18S/ITS sequencing can be used to diagnose bacterial infections and monitor outbreaks as acute infectious diseases remain one of the major causes of human diseases with high mortality. It can also be used to monitor and improve human health through gut or skin microbial diversity analysis. Nanopore-based 16S/18S/ITS sequencing can be applied to understand the role of microbes in agricultural, environmental, and health-related settings.

Nanopore-based 16S/18S/ITS sequencing workflow

Bioinformatics Analysis

Our general bioinformatics analysis workflow includes data pre-treatment, taxonomic assignment, diversity analysis, evolutionary analysis, and custom analysis, which is flexible to your needs.

Bioinformatics analysis Description
Data pre-treatment Quality control of the sequences, base calling
Taxonomic assignment Operation taxonomic unit (OTU) clustering, identification of species
Diversity analysis Classification and abundance analysis of single species and measurement of the difference in the bacterial community composition for different samples
Evolutionary analysis Construction of phylogenetic trees, estimation of genetic distance
Custom analysis Network analysis, correlation analysis, functional analysis, etc.

Sample Requirement

    1. DNA samples (concentration ≥ 100 ng/µL, 1.8 < OD260/280 < 2.0,2.0 < OD260/230 < 2.2) or cell suspensions
    2. Illumina platform: DNA amount ≥ 300 ng, PCR Products ≥ 400 ng
    3. PacBio platform: gDNA ≥ 100 ng, PCR Products ≥ 400 ng

Sampling kits: We provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: Raw sequencing data (FASTQ), trimmed and stitched sequences, quality-control dashboard, statistic data, and your designated bioinformatics report.


  1. Mataragas M, et al. A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods. Food Microbiology, 2018, 76: 279-286.
  2. Teppei Iwai, et al. Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer. FEBS Open Bio. 2019, 9(3): 548–557.
  3. Yang B, et al. Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC bioinformatics, 2016, 17(1): 135.
* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.

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