nanoCORE Amplicon Metagenomics

nanoCORE Amplicon Metagenomics is Microsynth’s end-to-end ONT-based sequencing service for microbial community profiling. Select from six validated marker regions to characterize bacterial (16S), archaeal (16S Archaea), or fungal (ITS) communities.

For added convenience, DNA extraction can be included for soil and fecal samples. Sequencing data are processed through our standardized bioinformatics pipeline, enabling species-level resolution for suitable marker regions and taxa.

Simply configure your project in the Microsynth webshop, receive instant pricing, and submit your order online – no quotation required.

Modular Workflow

Outsource the complete workflow or select specific modules. Our process is designed for flexibility. Typical steps include:

Raw data includes:

Sequencing quantity and quality assessment (.xlsx)
Raw sequencing data (.fastq per sample)
Summary report (.pdf)

Primer Systems

Choose the primer system that best fits your research focus.

Target Organism / Application	Primer System	Amplicon Size (bp)	Key Benefit
Bacteria (broadest coverage)	16S Advanced	~1500	Microsynth’s custom full-length 16S rRNA primer. Specifically designed to reduce bias and capture a broader bacterial diversity. Recommended as the default choice for bacterial profiling.
Bacteria	16S ONT	~1500	Full-length 16S rRNA gene using Oxford Nanopore’s kit primer. Compatible with ONT workflows but less comprehensive than Microsynth’s 16S Advanced primer.
Archaea	16S Archaea	~1000	Specifically optimized to amplify diverse and novel archaeal taxa from environmental samples.
Fungi & other Eukaryotes*	ITS1-4	~1200	Pan-eukaryotic metabarcoding based on full-length ITS. Useful for fungal and broader eukaryotic community analysis.
Fungi (optimized)	ITSFu	~1200	Tailored towards fungal ITS amplification. Recommended if fungal identification is your main focus.
Eukaryotes incl. fungi*	18S-ITS	up to 1500	Combines 18S fragment with full ITS sequences for pan-eukaryotic profiling including fungi.

*Note: Amplification may also capture non-fungal eukaryotic DNA (e.g. plants).

Bioinformatics Analysis

Our standardized bioinformatics workflow transforms raw ONT amplicon sequencing data into biologically meaningful insights, providing an intuitive overview of microbial community composition, diversity, and taxonomic structure.

The analysis results are delivered as a comprehensive set of publication-ready figures, interactive visualizations, and data files, including:

Comprehensive report (.html) – interactive summary with filtering and sorting functions
OTU sequences (.fasta) – full-length operational taxonomic units
Abundance and taxonomy tables (.tsv) – OTU counts, taxonomy assignments, and confidence scores
Diversity analysis (.tsv, .pdf) – intra- and intersample diversity metrics with rarefaction curves
Krona chart visualization (.html) – interactive graphical exploration of community composition
Principal component analysis (.tsv, .pdf) – overview of sample relationships and clustering
Statistical analysis visualizations – clear graphical representation of results

Example Results

All results are delivered in publication-ready figures and interactive formats, providing both high-level overviews and nucleotide-level detail.

Turnaround Time

Library preparation and sequencing only: 8 working days
Bioinformatics analysis: +2 working days
DNA isolation: +5 working days
Express processing is available on request, subject to feasibility

Sample Requirements

See User Guide

Custom Services (Available on Request)

If our standard nanoCORE service does not fully meet your project requirements, Microsynth also offers customized solutions. Depending on your needs, we can support additional sample types for DNA extraction, custom primer systems, and advanced bioinformatics analyses.

Please share your project requirements with us, and we will assess their feasibility and provide a customized quotation where appropriate.