Bacterial taxonomic profiling:
- 16S V1-V3
- 16S V3-V4
- 16S V3-V5
Fungal taxonomic profiling:
Archeael taxonomic profiling:
Besides the standard target list, available on our order page, we also have many more target regions, established in-house:
- plant ITS1
- plant trnL
- Different primer pairs for ITS2
- 16S bacteria V4
- 16S bacteria V5-V6
- Different primer pairs for: 16S bacteria V3-V4
Just get in contact with our local sales representative for more information.
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
- Earthy soil samples (no sand, sandy soil or sediment
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
Here we summarised all important information that you might need to know, when planning to order the INVIEW Microbiome Profiling 3.0.
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).
Please note that 16S primers can also amplify the loci of plant organelles.
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.