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16S Microbiome Profiling

Identify the microbial community in your sample

16S metagenomic analysis is mostly used for species profiling and species determination in a variety of environmental samples.

Most, if not all, bacteria can be differentiated by sequencing amplicons derived from one of the following regions: V1-V3, V3-V4 or V3-V5.

Eurofins Genomics offers all sets / regions as an NGS Favourite, that can be ordered online.


Specifications of microbial DNA Barcoding, available as online package

Basic service includes

  • 1x QC per sample (including real-time PCR to determine the bacterial content of your sample)
  • Amplicon generation (either V1-V3, V3-V4 or V3-V5)
  • Pooling & normalisation of amplicons
  • Sequencing on MiSeq with the 2 x 300 bp paired-end read module
  • Basic bioinformatic analysis (sorting of reads according to inline barcodes)
  • Data delivery
  • Minimum sample number: 6


As an additional service we will also purify the high molecular weight DNA from various starting material

  • Detection of pathogenic microorganisms
  • Fermentation surveillance (e.g. cheese)
  • Probiotics testing
  • Food / feed research (e.g. faeces)
  • Soil testing
  • Water / waste water testing
  • Microbial pollution in buildings
  • Aquaculture (e.g. microbiota in water, marine sediments)


 If required we also offer advanced bioinformatic analysis

  • 16S rRNA metagenome analysis
  • Taxonomical assignment and read abundance estimation for all OTUs down to species level (depending on the sample and bacteria present in the sample only down to genus or family level)
  • Normalised abundance estimation of bacterial and archaeal OTUs considering lineage-specific copy numbers of marker genes


Interested in other 16S regions or a custom project? Just contact us.

For pure cultures, we also offer classical bacterial species identification by DNA Barcoding of the 16S rRNA by PCR and Sanger sequencing.

Ordering 16S Microbiome profiling

Here we summarise all important information that you might need to know, when planning to order a 16S project.


General Information

  • Overlapping of reads might occur if you select sequencing of the v3-v4 region. For the other two regions the amplicon size is too long and no read overlapping will occur.
  • In our online order wizard you need to select one sequencing region. If you are interested in more than one region please order the package twice (with the different regions or double the amount of samples). In any case please add a remark for the NGS lab, so that they are able to assign the samples to the respective projects

DNA Extraction

  • For all projects where DNA extraction is required please read our sample submission guide carefully in order to avoid unwanted waiting times due to insufficient sample material.

Bioinformatic Related Information

  • Although sequencing 300 bp from each side, these 300 bp also include barcodes and base calls with poor quality. After clipping the reads will be approximately 40 bp shorter (also depending on the sample and thefore sequencing quality).
  • Taxonomical read assignment down to species level is dependent on several factors like: sample quality, sequencing quality, diversity in the specific genus / family and the 16S database. Due to these reason, a determination down to genus or family might only be possible for certain bacteria.
  • The reverse read is known to have a lower quality than the forward read. Therefore analysis might be more accurate by using only the forward read.
  • Taxonomical analysis will not be able to determine archea or cyano bacteria due to the current primer setup.