miCORE Amplicon Metagenomics

Uncover microbial diversity with targeted amplicon sequencing.
Amplicon metagenomics enables precise analysis of bacterial and fungal communities by focusing on taxonomic marker regions such as 16S rRNA and ITS. Whether comparing experimental groups, monitoring shifts, or characterizing unknown communities, this method provides accurate and efficient insights into microbial diversity.

What You Can Achieve

Explore bacterial, fungal, or archaeal community composition
Compare taxonomic shifts across experimental conditions
Detect nutrition-dependent microbiome changes (e.g., gut microbiota)
Characterize rare or environment-specific taxa (e.g., deep-sea archaea, airborne fungi)
Monitor community dynamics in bioreactors and other controlled systems
Optimize future sampling strategies with high-resolution data

Before You Start

To set up your amplicon metagenomics project effectively, consider:

Scientific objective – survey, experimental comparison, or functional inference?
Starting material – DNA, environmental sample, or need for DNA isolation?
Desired services – from DNA extraction to full bioinformatics analysis
Result type – raw data only, or full bioinformatics reporting

Our team supports you in selecting the optimal setup from design to analysis.

Modular Workflow

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

Bioinformatics Analysis

Without Bioinformatics

If you order sequencing only, you will receive:

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

With Standard Bioinformatics

Our standard 16S/ITS analysis module provides:

Comprehensive interactive report (.html)
Amplicon Sequence Variants (ASVs / zOTUs) in .fasta format
ASV abundance, taxonomy, prediction confidence (.tsv, .xlsx)
Intrasample diversity & rarefaction curves (.tsv, .pdf)
Interactive Krona charts for taxonomic exploration (.html)

Complementary Bioinformatics (optional, additional costs)

Comparative Analysis

Inter-sample diversity & clustering (.tsv, .pdf)
Principal Component Analysis (PCA) of sample relationships (.tsv, .pdf)
Differential ASV analysis with statistics (.tsv, .html)
Visual summaries of statistical results

Functional Profiling

Prediction of functional profiles based on identified taxa (.tsv, .html)

Example Results

[below] from left to right

Alpha diversity analysis: observed richness, Chao1 estimates, and Shannon diversity indices
Interactive taxonomic visualization : Krona chart of microbial community composition
Community clustering: PCA plot based on UniFrac distances, grouping samples by condition
Taxonomic table: relative abundances, classification confidence values

[second row]

Differential abundance table: statistical comparison of OTUs/ASVs between groups
Functional profiling table: predicted pathways and their occurrence across samples

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