Identify the microbial community in your sample
Our Microbiome Profiling Favourites offer a highly sensitive identification and classification of the microbial population in a variety of environmental, food or clinical samples.
To accomplish that, Eurofins Genomics is amplifying and Illumina MiSeq sequencing the hypervariable regions of the 16S rRNA gene or the fungal internal transcribed spacer (ITS) gene.
For your individual profiling project, you may select one or several target/s from the following list:
• 16S: V1-V3, V3-V4 & V3-V5
• ITS: ITS1 & ITS2
Choose one or several 16S targets to analyze the bacterial content in your samples, and choose one or two ITS target to analyze the fungal content.
You prefer for some reasons another target region(s)?
Just do the first target-specific PCR step in your own lab, and let Eurofins continue with purification of PCR the products, the index PCR and sequencing. This “ 2nd PCR Microbiome Profiling Favourite” offers full flexibility of the target region combined with cost-effective outsourcing of the remaining processes.
Interested in a custom project with other target regions and your own sequencing run? 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.
Specifications of Microbiome Profiling Favourites, available as online package
Microbiome Profiling with 1-4 targets
- Generation of 1 – 4 Amplicons per sample (choose from three 16S and two ITS targets) using a two-step PCR protocol
- Pooling & normalisation of amplicons
- Sequencing on MiSeq with the 2 x 300 bp paired-end read module
- Delivery of on average 80.000 – 90.000 cluster (read pairs) per amplicon
- Sorting of reads according indices and data delivery
- Minimum sample number: 6
2nd PCR Microbiome Profiling
- You prepare the 1st, target specific PCR in your own lab
- Purification of each amplicon sent in
- Index PCR
- Pooling, Sequencing, etc. as described above
- Minimum sample number: 6
As an additional service we offer extraction of high molecular weight DNA from various starting material
- Fermented products, cheese or yoghurt
- Enrichment cultures / starter cultures
- Buccal swabs
- Human and animal faeces
- Water & waste water
- Soil & dust samples
If required we also offer advanced bioinformatic analysis:
- Pre-processing of reads & chimera filtering
- Merging of overlapping paired reads (depending on size of target region)
- Picking of OTU representative sequences (Operational Taxonomic Unit)
- Taxonomical assignment and read abundance estimation for all detected OTUs down to species level (if possible)
- Normalised abundance estimation of bacterial OTUs considering lineage-specific copy numbers of marker genes
Ordering Microbiome profiling
Here we summarised all important information that you might need to know, when planning to order a Microbiome Profiling Favourite.
- Overlapping of reads might occur if you select a short target region (e.g. v3-v4 region). For the longer regions the amplicon size is too long and read overlapping will not occur or only for some of the read pairs.
- Each 16S and ITS primer combination fails to amplify certain species. The use of multiple primer combinations is recommended to capture the entire community (e.g. Ihrmark et al., 2012; Toju et al., 2012).
- 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 base calls with poor quality. After clipping the reads will be approximately 40 bp shorter (also depending on the sample and the 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 nucleotide database. Due to these reasons, a determination down to genus or family might only be possible for certain bacteria.
- Taxonomical analysis will not be able to determine archea or cyano bacteria due to the current primer setup.
For more information please also have a look at our FAQs.