Shotgun Metagenomic Sequencing
Untargeted DNA sequencing for deeper microbiome insight
Shotgun metagenomic sequencing is used when you want to profile the DNA in a sample more broadly than with marker-gene sequencing. Instead of targeting one selected region, shotgun sequencing reads DNA across the sample, making it possible to study both taxonomic composition and functional potential.
At Biomcare, shotgun metagenomic sequencing can be delivered as a standalone sequencing service or combined with bioinformatics, statistical analysis and reporting. This makes it suitable both for customers who already have their own analysis pipeline and for projects where interpretation and decision-ready outputs are needed.
When shotgun metagenomic sequencing is a good fit
Shotgun metagenomics is relevant when you need more than targeted bacterial or fungal profiling.
It is often used when:
- you need both taxonomic and functional profiling
- species-level or strain-level insight is important
- you want to investigate genes, pathways or microbial functions
- you need broader profiling across microbial groups
- you are working with complex samples such as soil, water, gut/stool, plant, root or bioreactor material
- you want whole-genome information from isolates
- you need a stronger basis for downstream bioinformatics and statistical analysis
The level of detail depends on sample type, sequencing depth, DNA quality, database coverage and the analysis strategy. We help clarify this before the project is started, so the sequencing setup matches the question you want answered.
What we offer
| Sequencing type | Untargeted whole-DNA sequencing |
|---|---|
| Profiling | Taxonomic profiling and functional profiling where relevant |
| Resolution | Species-level or strain-level insight depending on sample, data depth and analysis setup |
| Sequencing platforms | Short-read sequencing, including Illumina, and long-read approaches such as Oxford Nanopore or PacBio where relevant |
| Typical outputs | Raw FASTQ files, quality-filtered data, taxonomic profiles, functional profiles, figures, tables and reports depending on project scope |
| Sample types | Soil, water, plant, root, gut/stool, skin, blood, sputum, biopsies, cultures, isolates and bioreactor samples |
| Optional add-ons | DNA extraction, spike-in based absolute quantification, genome assembly, functional profiling, statistics and reporting |
What you get
For sequencing-only projects, we can provide extraction, library preparation, sequencing and raw FASTQ files.
For projects where you need analysis support, Biomcare can also provide:
- data quality evaluation
- quality filtering
- taxonomic profiling
- functional profiling of genes, pathways or other features
- statistical analysis based on project metadata
- publication-ready figures and tables
- reports describing the data, workflow and results
Advanced option: metatranscriptomics
For some projects, DNA-based profiling is not enough. If you want to investigate which genes are actively expressed at the time of sampling, metatranscriptomics may be relevant.
Metatranscriptomics requires careful planning around RNA preservation, sample handling, storage and timing. We recommend discussing this before sampling begins.
Request a sequencing quote
Send us information about your sample type, number of samples, project aim and whether you need raw data only or downstream analysis. We will help you identify a sequencing setup that fits the question you want answered.
