Important note for all re-orderers (21.12.2019):
- Eurofins recently optimised the microbiome workflow. Consequently we defined new sample preparation and ordering guidelines.
- This includes the shipment container and the required use of NGS barcodes.
- Furthermore we optimised the target specific primer sequences for our V3-V5 and the archeae target region to enable a better taxonomical assignment and reproducibility.
- For the 2nd PCR otpion, where you prepare the amplicons in your own lab, we changed the adaptor sequences that you need to add to the target specific sequences
- Please read the sample preparation guide carefully.
- In case you have any questions regarding those modifications or need assistance due to the changed ordering process / order sheet, please don't hesistate to contact our support team.
Identify the microbial community in your sample
Our InView Microbiome Profiling 3.0 offers 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 region(s) from the following list:
Bacterial taxonomic profiling:
• 16S: V1-V3, V3-V4 and V3-V5
Fungal taxonomic profiling:
• ITS: ITS1 and ITS2
Archeael taxonomic profiling:
• 16S target
You prefer for some reasons another target region(s)?
Just prepare the amplicons in your own lab, and let Eurofins continue with the indexing and sequencing. This option 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 the InView Microbiome Profiling 3.0
Microbiome Profiling with 1-4 targets
- Generation of 1 – 4 amplicons per sample (choose from our target list) 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 & primer sequence clipping
- Merging of overlapping paired reads (depending on size of target region)
- Data delivery via FTP server upload
- Minimum sample number: 1
2nd PCR Microbiome Profiling
- You perform a target specific PCR in your own lab and purify the DNA (preferred in EB buffer)
- Indexing of all samples @ Eurofins Genomics
- Pooling, Sequencing, etc. as described above
- Minimum sample number: 1
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
- 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 and archaeal 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 the InView Microbiome Profiling 3.0.
- 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 organisms.
- Taxonomical analysis will not be able to determine cyano bacteria due to the current primer setup.
For more information please also have a look at our FAQs.