Customer-friendly solutions

- to complex problems

DNA sequencing and bioinformatics made easy
- we provide tailored sample-to-answer solutions

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

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

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

  • Please find a collection of sampling protocols at https://www.midasfieldguide.org/guide/protocols

  • 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.

  • Primer 1: 10 x 150 EUR =  1500 EUR
    Primer 2: (10 x 150 EUR) x 10% discount =  1350 EUR
    Total =  2850 EUR

  • 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.

  • 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.

  • Yes, we also offer to sequence any functional gene of interest. Contact our experienced staff to discuss your project in detail.

  • Yes, is possible to use a custom database. Contact our experienced staff to discuss your project in detail.

  • 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.

  • 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).

Wagma Saei, MSc.
Research Scientist

For more details please check out our microbial community analysis product sheet

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