miCORE Whole Genome Metagenomics

Considerations before starting a shotgun metagenomics project:

• Sample Source and Quantity: How much sample material is available, and what is its origin?
• Sequencing Depth: What level of sensitivity is required to capture your target organisms?
• Community Complexity: How diverse is the biological community, and what is its composition?
• Research Focus: Are you exploring genetic potential, taxonomy, or both? Should your profiling include functional insights?
• Study Type: Will your project be descriptive, empirical, or a combination of both?
• Methodology: Is Whole Genome or Amplicon Metagenomics better suited to your goals?
• Data Analysis: Do you have access to the necessary computational resources and bioinformatics expertise?

Let us guide you – from design to analysis

Example projects using shotgun metagenomics:

• Analyzing soil microbial communities
• Investigating community shifts and genomic changes under altered environmental conditions or hosts
• Exploring evolutionary adaptations in micro-environments
• Conducting gene-level analysis of uncultivatable microbial communities
• Detecting viruses in mammalian tissues and exudates

Applications related to shotgun metagenomics:

• miCORE Amplicon Metagenomics
• nanoCORE Amplicon Metagenomics
• Shotgun Metatranscriptomics
• BacterialSeq

For further technical description and how to order, please download our User Guide miCORE Whole Genome Metagenomics (see related downloads ).

Unlike amplicon-based metagenomic studies, Whole Genome Metagenomics does not rely on a single phylogenetic marker gene. Instead, it analyzes all DNA present in a sample, allowing for the simultaneous identification and relative abundance of organisms from all biological domains.
Whole Genome Metagenomics goes beyond determining the taxonomic composition of a community; it also uncovers its functional gene inventory, providing valuable insights into the biological potential of the system.

Analyzing Whole Genome Metagenomics datasets can be challenging due to their large size. The most demanding step is read alignment against reference databases, which requires powerful hardware and sophisticated and optimized bioinformatics solutions. Our Whole Genome Metagenomics analysis module employs high-performance servers and cutting-edge tools to ensure efficient data processing. This module can help you answer key questions such as:

1. What is the taxonomic composition of the microbial community, including both eukaryotic and prokaryotic organisms? (See Figure 1)
2. How do the sample cluster based on their microbial community composition? (See Figure 2)
3. What is the functional potential of the microbial community? (See Table 1)

Figure 1: Picture of an interactive Krona chart depicting the microbial community yielded from analyzing a soft cheese sample. Click on the Image for the interactive version featuring additional samples (soft cheese, hard cheese, lichens)

Figure 2: Correlation matrix detailing sample correlation coefficients (Pearson correlation) and clustering of the samples corresponding to the results shown in Fig. 1.

Table 1: Functional potential of the analyzed samples characterized by detected Enzymes (only a small subset is depicted)

• Data delivery within 20 working days after sample receipt (includes library preparation and sequencing).
• An additional 15 working days for full data analysis (bioinformatics) or 5 working days for taxonomy analysis only.
• Express service available upon request.