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Nanopore-Based 16S rRNA sequencing

Our Nanopore-based full-length 16S ribosomal RNA (rRNA) sequencing applies a direct PCR strategy that can directly go on PCR amplification of 16S rRNA genes from bacterial/archaeal cell suspensions without DNA purification. The approach overcomes the limitations of traditional culture-based bacterial identification and can provide rapid and accurate bacterial/archaeal identification and diversity analysis.

Our Advantages:
  • Rapid and easy streamlining workflow to identify bacteria and archaeal at the species level.
  • Rapid and economical sequencing: the 16S rapid amplicon barcoding kit contains 12x barcoded primer pairs for multiplexing samples, enabling even more cost-effective results.
  • Long reads enable more efficient analysis and removal of potential sources of bias.
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Nanopore-based 16S rRNA 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 identification of prokaryotes by using molecular techniques such as PCR and sequencing. Nanopore sequencing, a long-read sequencing technology, has obvious advantages in generating a more accurate profile of 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 rRNA sequencing provides rapid and accurate prokaryotic identification analysis by nanopore sequencing with a relatively simple workflow and no need for DNA purification.

Nanopore-based 16S rRNA sequencing is a novel molecular approach for the taxonomic characterization of microbial communities in a more comprehensive and rapid manner. In clinical microbiology, nanopore-based full-length 16S rRNA 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 rRNA sequencing has comprehensive applications to understand the role of microbes in agricultural, environmental, and health-related settings.

Nanopore-based 16S rRNA 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

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.

Areas of Interest

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