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.
We have extracted DNA from all types of low- and high-biomass sample matrices. Our DNA extraction workflows can be customized (using both manual and automatic methods) to accommodate most sample types while minimizing DNA extraction biases in complex communities (see Albertsen et al.) and preserving yield and quality (purity and HMW DNA) to the widest possible extent. Our DNA extraction expertise guarantees the most optimal project outcome and is compatible with both short-read (Illumina) and long-read sequencing platforms (e.g., Oxford Nanopore sequencing).
Sample matrices (non-exhaustive list): Prokaryotes, invertebrates, fungi, salmon, wastewater, aquacultures, soil, oil spills, marine/freshwater samples, eDNA (environmental DNA), bioreactors, tree bark, mangrove and marine sediments, pig/chicken/rat/fish entrails/feces, mining/drill sites, cow rumen, seaweed, oysters, mouthwash, tooth swaps, skin swaps, microbial induced corrosion samples, lung tissue, colon cancer biopsies and liver biopsies.
Our standard package includes: Optional pre- and post-project meetings with a DNASense specialist, standard turnaround time (5 weeks), DNA extraction, quality control, DNA library preparation, Oxford Nanopore (R10.4.1) long-read sequencing or Illumina MiSeq sequencing with 2X301 bp, 50.000 reads, 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.
Add-on services (non-exhaustive list): Increased read depth, 3 or 7 workday fast turnaround time (Oxford Nanopore Technologies only), LEfSe (Linear discriminant analysis Effect Size), and extended statistical analysis.
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.
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.
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).