The sample analysis process

Once the intake procedure has been finalized, you will receive an email containing a registration document and instructions on how to provide samples. It is important that you spend time to read the instructions, as the very specific protocols ensure the most reliable final results. You then return the sample information to us and the details are entered into the MiCA database. The physical samples themselves can then be shipped to MiCA or delivered to us in person where they are put into cold storage at either -20C or -70C until processing.

1. DNA Extraction

2. Amplification and Illumina library preparation

3. Sequence Data Processing

4. Besides the raw sequence data, ASV tables


The 16S gene is a ribosomal RNA gene which is a universal marker gene for all bacteria and archaea. The gene s composed of conserved and variable regions making it an ideal universal target for untargeted microbial profiling.
These main features are important because based on the conserved residues we can amplify the information. Between the conserved regions lie variable regions which contain all the information which is discriminatory between the bacteria: those variables are thus the markers for which bacteria one is dealing with. This is used as a basis for looking at the microbial communities.

At Microbiota Center Amsterdam we sequence the V3-V4 regions of 16S gene because this region has the broadest specificity with the best possible phylogenetic resolution within the technical restrictions of Illumina MiSeq sequencer.


For fungi we sequence ITS. ITS is an intergenic region which means it is hypervariable as there is little selective pressure on it. This in turn means that ITS sequencing gives an extremely high taxonomic resolution for whichever fungi you are dealing with.


Read more about biological data