Microbial Community Analysis
Studying the microbial community in any given type of sample is now feasible by next generation sequencing. It is possible to identify and analyze the bacterial, archaeal, fungal, and eukaryotic composition by sequencing of the 16S/18S rRNA gene and the ITS gene. Our optimized workflows offers the possibility to target different variable regions of the 16S gene e.g. V1-3, V3-4, V4, V3-5 and many others, to provide the best possible analysis of a specific community belonging to any given environment. We have a variety of databases that we use depending on the sample type e.g., MiDAS, SILVA, and HOMD. Standard analysis provides the possibility for taxonomic classification to genus level. Our easy-to-use analysis tool DNASense app gives you free hands to experiment with your data set and draw further conclusions.
With our optional pre-project online meeting, it is possible for you to discuss the best suited analysis strategy with one of our product specialists.
The microbial community analysis package “from sample to answer” includes:
- DNA extraction
- Quality control
- Library preparation
- Illumina MiSeq sequencing with 2X301 bp
- Scaled for 50,000 raw reads for 16S rRNA genes
- ASV/OTU clustering, relative abundance estimates and taxonomic classification
- Statistics and microbial community analysis presented as heatmaps and PCA plots.
- Free access to our DNASense App
- Optional pre- and post-project meeting with a DNASense specialist
- Add-on services as additional statistical analysis available e.g., LEfSe (Linear discriminant analysis Effect Size)
- Near full-length 16S rRNA gene (V1-8) sequencing using Oxford Nanopore Technologies platform available
- Standard turnaround time (TAT): ~5 weeks – see below for fast-track options
List prices in EUR
List prices in DKK
List prices in EUR
Oxford Nanopore Technologies long-read sequencing*
| Extraction | Sequencing | Raw data + QC | Data analysis + app access | Price/sample (EUR ex vat) | ||
|---|---|---|---|---|---|---|
| ≥ 10 samples | ≥ 50 samples | ≥ 100 samples | ||||
| 170 | 145 | 130 | ||||
| 150 | 130 | 115 | ||||
| 135 | 115 | 100 | ||||
Illumina short-read sequencing
| Extraction | Sequencing | Raw data + QC | Data analysis + app access | Price/sample (EUR ex vat) | ||
|---|---|---|---|---|---|---|
| ≥ 10 samples | ≥ 50 samples | ≥ 100 samples | ||||
| 150 | 125 | 110 | ||||
| 135 | 115 | 100 | ||||
| 120 | 100 | 90 | ||||
*MCA fast-track options (Oxford Nanopore Technologies only):
TAT ≤ 7 workdays, 1200 EUR per project fee
TAT ≤ 3 workdays, 2020 EUR per project fee
List prices in DKK
Oxford Nanopore Technologies long-read sequencing*
| Extraction | Sequencing | Raw data + QC | Data analysis + app access | Price/sample (DKK ex vat) | ||
|---|---|---|---|---|---|---|
| ≥ 10 samples | ≥ 50 samples | ≥ 100 samples | ||||
| 1250 | 1060 | 940 | ||||
| 1125 | 960 | 845 | ||||
| 1000 | 850 | 750 | ||||
Illumina short-read sequencing
| Extraction | Sequencing | Raw data + QC | Data analysis + app access | Price/sample (DKK ex vat) | ||
|---|---|---|---|---|---|---|
| ≥ 10 samples | ≥ 50 samples | ≥ 100 samples | ||||
| 1100 | 935 | 825 | ||||
| 990 | 840 | 740 | ||||
| 880 | 750 | 660 | ||||
*MCA fast-track options (Oxford Nanopore Technologies only):
TAT ≤ 7 workdays, 9000 DKK per project fee
TAT ≤ 3 workdays, 15000 DKK per project fee
FAQ
How do I sample representatively from activated sludge, digester sludge or influent wastewater?
Please find a collection of sampling protocols at https://www.midasfieldguide.org/guide/protocols
How much sample should I send?
The amount of sample depends on the sample type. If you have water samples we would recommend to sample 100-1000 mL. If the water has a high density of bacteria approximately 100 mL should be fine but if the water is very low in bacterial density we would recommend to sample at least 1000 mL. Alternative to send a large volume of water you can filter the water sample on a 0.2 µm filter.
I have 10 samples which I would like to have sequenced with 2 different primers. What would the price be? (Illumina short-read sequencing price example)
Primer 1: 10 x 150 EUR = 1500 EUR
Primer 2: (10 x 150 EUR) x 10% discount = 1350 EUR
Total = 2850 EURWhich 16S rRNA variable gene region should I use as my target region to have sequenced?
The variable region depends on the type of sample and if you have some specific organisms you would like to target. E.g. if you are interested in nitrifying bacteria in activated sludge we would recommend to sequence the variable gene region 4 (V4 region). Also if you have both bacteria and archaea in your sample you could have both sequenced with a modified primer set targeting the V4 region in both bacteria and archaea, however, these primers underestimate the proportion of archaea so if the full diversity of archaea is of interest we would recommend using specific archaea primers targeting the V3-V5 region.
I have a specific gene region I would like to have sequenced do you offer this?
Yes, we offer to sequence the gene region of your choice. If we do not have the specific primers in-house, we offer to purchase them on our own expense.
Do you offer to sequence functional genes?
Yes, we also offer to sequence any functional gene of interest. Contact our experienced staff to discuss your project in detail.
I have a custom database, can you use this for taxonomic classification?
Yes, is possible to use a custom database. Contact our experienced staff to discuss your project in detail.
I have +100 samples, do you offer an additional discount? (Illumina short-read sequencing price example)
For projects with +50 samples (1 primer set) we offer an additional discount of 15 %. The price would then be: 150 Euro x 100 samples * 15 % discount = 12,750 Euro.
If you do not need the DNA extraction, we offer an additional discount of 10 % and the price would then be: 150 Euro x 100 samples * 25 % discount = 11,250 Euro.Can I achieve taxonomic classification to species level?
This is highly dependent on not only the variable region of choice, but also the reference database. For OTUs defined at the 97% identity threshold and with a good reference database, genus-level resolution can be expected. For higher resolution (species), an ASV workflow can be pursued. However, taxonomic classification is still limited by the reference database (i.e. species-level classification cannot be achieved for a genus-level reference database).
Research Scientist
For more details please check out our microbial community analysis product sheet