Shotgun Metagenomic Sequencing

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Detailed sequencing of microorganisms

Shotgun metagenomic sequencing provides a detailed picture of the composition of microorganisms in a sample. As opposed to amplicon-based methods like 16S rRNA sequencing, shotgun sequencing covers microorganisms from different kingdoms of life and increases the resolution by providing information on strain level variation.

In addition to providing detailed information on which organisms are found and their relative abundance, this sequencing solution also profiles the genetic content of the microorganisms thereby providing information on the functional potential of the microbiome in a sample. Simply put, it tells you both who is there and what they can do.

By applying our data processing and biostatistical platform, we can evaluate if a certain test condition, such as a new food ingredient, affects the composition and function of the microbiome, and detect which specific genes and pathways are involved.

Why chose shotgun metagenomic sequencing?

  • Higher resolution as compared to amplicon sequencing (16S and ITS). Shotgun sequencing can provide information on organisms down to strain level while 16S/ITS is limited to genera or, in ideal cases, species-level information.
  • Information on both taxonomy and function (genes and pathways).

*Please note the option to use spike-in solutions for the calculation of absolute abundance. By default, sequencing methods provide information about the relative abundance of microorganisms in a sample. By using spike-in of known concentrations of microorganisms, we can calculate the actual number of organisms in a sample.

Solving your microbiome problems

We have more than +7 years of experience in analyzing microbiome data and structuring microbiome projects. Our team has worked on more than 75 microbiome projects spanning research, universities and commercial industries.

Biomcare offers both microbiome services for small discovery projects, as well as large custom-designed microbiome projects.

Contact us today and get a quote. We are standing by to service you.

What we do

  • DNA extraction
  • Shotgun metagenomic sequencing on a HiSeq Illumina platform
  • Data quality evaluation and quality filtering to prepare the data for microbiome profiling
  • Microbiome profiling – calculation of the relative abundance of specific organisms and functional features in the samples
  • Statistical analysis

What you get

For each project, a private project folder is made available on the Biomcare server, where all resulting data, statistical results, illustrations, reports, etc. are available for download.

Sample collection barcodes, tubes, or kits

Depending on the type of tissue you collect, we will ship barcode stickers or barcode-labeled tubes. For larger clinical projects, we can provide collection kits if requested.


  • Raw sequencing data in fastq format
  • Quality filtered data in fastq format

Results reports

Three reports are generated with all necessary information on sequencing, data processing, and statistical analysis, and all resulting results, illustrations, and tables.

  1. A report describing the performed sequencing, data evaluation, and processing
  2. A report describing the generated microbiome profiles, and first microbiome evaluations
  3. A report describing the statistical analysis performed and the results, including illustrations and tables.


Personal guidance and communication

A key factor for successful outcomes of every project is communication. Every project is different, and good personal communication allows us to understand exactly what our customers wish to achieve. This is especially essential when we design the statistical analysis and incorporate customer-provided information.

We typically have the most active communication at the beginning when samples are being collected and shipped, and then again when statistical analysis is initiated, and results start to emerge.

At the end of the project, we present the project results in an online or face-to-face meeting, depending on geographical circumstances and project size/complexity.

Biomcare was involved from study design, over shipment, sequencing, data analysis and interpretation.

Annette Vestergaard

Senior specialist - soil and soil management