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miCORE Whole Genome Metagenomics

Shotgun Metagenomics
 
 
Unbiased community profiling. Reveal taxonomy and function at species- or strain-level precision. Transcend domain boundaries for a truly comprehensive view.
From soil and water to host-associated samples, shotgun metagenomics enables comprehensive analysis of all DNA in your sample. Go beyond marker genes to uncover taxonomic composition, metabolic potential, and functional elements such as antibiotic resistance and virulence factors.



 

What You Can Achieve

  • Characterize bacterial and fungal communities
  • Identify organisms and estimate relative abundances down to species or strain level
  • Detect viruses in complex samples, including host tissues and exudates
  • Explore metabolic functions, e.g., antibiotic resistance genes,virulence factors, etc.
  • Conduct gene-level analysis of uncultivable microorganisms
  • Track community shifts and evolutionary adaptations under changing conditions

Before You Start

To set up your shotgun metagenomics project effectively, consider:

  • Sample source and quantity – origin and amount of material available
  • Sequencing depth – level of sensitivity needed to detect rare organisms
  • Community complexity – taxonomic diversity and expected composition
  • Research focus – taxonomy, function, or both
  • Method choice – is Whole Genome Metagenomics or Amplicon Metagenomics the better fit?
  • Data analysis – availability of computational resources and bioinformatics expertise

Our experts support you from experimental design to bioinformatics analysis.

Modular Workflow

Outsource the complete workflow or select specific modules. Our shotgun metagenomics process is designed for flexibility.

Typical workflow steps include:

Shotgun Metagenomics Workflow

Bioinformatics Analysis

Our Whole Genome Metagenomics analysis module combines intensive computing with optimized tools for reliable results. Typical analyses include:

  • Data quality control
  • Taxonomic profiling of organisms from all biological domains
  • Clustering of samples based on community composition
  • Functional annotations
  • Visualization with interactive charts (e.g., Krona plots)

Example Results

Krona Chart

[left] Click to explore the interactive Krona chart showing taxonomic composition from domain to species level.






[below] from left to right

  • Boxplots of alpha diversity metrics per sample group
  • Heatmap showing sample-to-sample correlations.
  • PCA plot visualizing differences in microbial community composition between samples.
  • Subset of detected enzymes in the samples.
Sankey diagram

[left] Click to explore the interactive Sankey diagram showing enzyme distribution across organisms.

 

Turnaround Time

  • Sequencing only: 20 working days
  • Full analysis: +15 working days
  • Taxonomy-only analysis: +5 working days
  • Express service available upon request

Sample Requirements

  • Buffer recommendation: 10 mM Tris-HCl (pH 7.5–8.5)
  • Avoid: EDTA >1 mM
  • DNA quantification: Fluorometric methods (e.g., PicoGreen®, Qubit®)
  • Please contact us for project-specific input on DNA amount and quality

Notes