Metagenomic sequencing is an advanced research technique used to analyse complete sets of genetic material from diverse microorganisms inhabiting a specific environment, such as soil, water, the gut or skin. Metagenomic Seq enables all microorganisms present in a sample to be investigated without prior culturing in the laboratory. This approach provides detailed information about microbial biodiversity, functions and interactions within a given ecosystem.
Metagenomic Seq workflow
01Sample collectionThe first step is to collect a sample from the environment of interest. This may be a water or soil sample, a sample from the gastrointestinal tract, skin or other tissue.
02DNA extractionTotal DNA is isolated from the collected sample. This is a critical step because all DNA from microorganisms such as bacteria, viruses and fungi must be extracted without contamination.
03Library preparationDNA fragmentation, followed by addition of sequencing adapters and indexes (enabling multiplexing).
04Sequencing: Analysis on Illumina, ONT and PacBio.
05Bioinformatics analysisTaxonomic identification and detection of pathogenic microorganisms or genes associated with antibiotic resistance.
Applications of Metagenomic Seq
01Human microbiome studies - Metagenomic sequencing is widely used to study the human microbiome, including the gut, skin and respiratory microbiomes. It helps us understand the role of microorganisms in human health, including their effects on digestion, immunity and diseases such as obesity, diabetes and inflammatory bowel disease.
02Environmental monitoring - Metagenomics is used to study microbial biodiversity in natural ecosystems such as soils, groundwater, rivers and lakes. It enables assessment of the impact of pollution on microorganisms and monitoring of changing environmental conditions.
03Pathogen testing - This method enables rapid detection of novel pathogens that may be difficult to identify using conventional microbiological methods. It is used, among other applications, to diagnose infectious diseases and identify pathogens in clinical samples.
04Biotechnology and industry - Metagenomics is used to search for novel enzymes, proteins and metabolites with potential applications in the food, pharmaceutical and energy industries. These studies enable the discovery of new biological resources from natural microorganisms.
05Agriculture and bioremediation - In agriculture, metagenomics helps us understand how microorganisms affect plant health, support pesticide biodegradation and improve soil quality. It can also be used for bioremediation, that is, removing chemical pollutants from the environment using microorganisms.
Technical specifications of Metagenomic Seq
Specifications: Illumina
- Sequencing mode: 2x150 bp
- Amount of data per sample (output):
- 6 Gb of data per sample - standard, recommended approach
- 10 Gb of data per sample
- 20 Gb of data per sample;
- Other / Custom (available upon special request).
- Recommended Sample Requirements - DNA/RNA (Illumina):
- Sample type: gDNA
- Amount: > 50 ng
- Concentration (NanoDrop): >20 ng/μL
- Volume: >20 μL
- Purity (OD260/280): 1.6 - 2.5
- MINIMUM Sample Requirements - DNA/RNA (Illumina):
- Sample type: gDNA
- Amount: > 30 ng
- Concentration (Qubit): >1 ng/μL
- Volume: >20 μL
DNA extraction from submitted samples is also available. Details here.
Specifications: PacBio
- Long reads, 8kb
- Amount of data per sample (output):
- 10 Gb of data per sample - standard, recommended approach
- 20 Gb of data per sample
- Other / custom (available upon special request).
- Recommended Sample Requirements - DNA/RNA (PacBio):
- Sample type: gDNA
- Amount: > 15 000 ng
- Concentration (NanoDrop): >50 ng/μL
- Volume: >20 μL
- Purity (OD260/280): 1.6 - 2.5
- MINIMUM Sample Requirements - DNA/RNA (PacBio):
- Sample type: gDNA
- Amount: > 10 000 ng
- Concentration (Qubit): >50 ng/μL
- Volume: >20 μL
DNA extraction from submitted samples is also available. Details here.
Specifications: ONT
- Long reads, 10kb
- Amount of data per sample (output):
- 6 Gb of data per sample - standard, recommended approach
- 10 Gb of data per sample
- Other / custom (available upon special request).
- Recommended Sample Requirements - DNA/RNA (ONT):
- Sample type: gDNA
- Amount: > 3 000 ng
- Concentration (NanoDrop): > 50 ng/μL
- Volume: >20 μL
- Purity (OD260/280): 1.6 - 2.5
- MINIMUM Sample Requirements - DNA/RNA (PacBio):
- Sample type: gDNA
- Amount: > 2 000 ng
- Concentration (Qubit): > 40 ng/μL
- Volume: >20 μL
DNA extraction from submitted samples is also available. Details here.
Metagenomic Seq bioinformatics analysis
The advanced bioinformatics analysis The metagenomic sequencing package includes, among other analyses:
- Functional annotation: Nr, GO, KEGG, eggNOG, Pfam, SwissProt, CAZy, CARD, PHI-base, CYPED, QS, BacMet
- Biodiversity analysis at the functional and species levels
- Composition and relative abundance
- Alpha and beta diversity analysis
- Between-group differential analysis
- Correlation and association analysis
Selected projects and client publications
See which institutions we perform next-generation sequencing (NGS) for and explore scientific publications that draw on the data we have supplied.
Selected publications (1 publication)
INSTITUTION
SCOPE OF WORK
PROJECT YEARS
PUBLICATIONS (JOURNAL, YEAR)
PROJECT YEARS
2025
PUBLICATIONS (JOURNAL, YEAR)10.3390/ijms27072960 ↗
International Journal of Molecular Sciences, 2026
Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota
doi.org/Selected projects (5 orders)
INSTITUTION
SCOPE OF WORK
PROJECT YEARS
PROJECT YEARS
2025
PROJECT YEARS
2025
SCOPE OF WORKMetagenomic Sequencing
PROJECT YEARS
2025
PROJECT YEARS
2025
PROJECT YEARS
2024
To protect client confidentiality, we show only selected projects for public-sector institutions that are not covered by non-disclosure agreements (NDAs).
Last updated: 12 November 2026
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