DNA sequencing of microorganisms and microflora

Purpose

The sequencing technique is used, for example, to identify the source of a microbiological contamination in a production facility, or to characterize the presence of resistance genes in an isolated bacterium. In addition to analysis of disease-causing and spoilage / product-destroying microorganisms, we also work with desirable microorganisms in products and industrial processes. We can, for example, follow the development and quality impact of the microbiological flora during a fermentation process and during storage of the product.

We at RISE perform sequencing assignments for projects with viruses, bacteria, yeast and mold, as well as to determine antimicrobial resistance. We have cutting-edge expertise regarding sampling and extraction of DNA from microorganisms in complex samples, as well as a great understanding of our customers' needs and opportunities. Our practical and theoretical knowledge has been built up through our own research and close collaboration with industry in applied research and commissioned projects.

We can help with all or part of your sequencing project, including this:

• Sampling plan and choice of sequencing technology to optimize the conditions to be able to solve the customer's challenge.
• Sampling of microorganisms in complex environments and products.
• Sample preparation and extraction of DNA in laboratories classified according to Bio Safety Level 2 (BSL2).
• Whole genome sequencing of bacterial isolates for identification, transmission routes,
• Amplicon sequencing of 16S rDNA and / or internal transcribed spacer (ITS) to characterize the composition of the microflora. The choice of amplicon is adapted to the project objectives.
• Metagenomics for characterization of unknown microorganisms and the composition of the microflora.
• Bioinformatics analysis and comparative genomics for product development, quality control, benchmarking, source identification and tracing, etc.
• Comparison of similar strains, analysis of variance including SNP analysis, MLST and cgMLST etc.
• Interpretation of data and advice on decision-making based on produced sequence data

Method

We use modern sequencing technologies based on a technology called next-generation sequencing (NGS) or massive parallel sequencing (MPS). According to the clients' needs, we apply, develop and adapt microbiological methods from sampling and extraction of DNA via sequencing and data processing to meaningful results.

Project overview DNA sequencing

1. Sample from product / process / environment
   A representative sample is taken from what is to be examined. We routinely handle samples from, e.g., food, processes, water, the environment, clean cultures. Microbial DNA is extracted, purified and concentrated.
2. Sequencing
   Extracted DNA is fragmented, prepared and placed in a sequencing instrument that reads the DNA sequence, i.e. sequenced. By reading the DNA fragments many times, the entire genome can finally be mapped.
3. Bioinformatics
   Using powerful computers and bioinformatics programs, the extensive amount of data generated during sequencing is monitored and filtered. Usually, the genome is then recreated digitally based on the resulting DNA sequences. The genome is compared with the reference genome of the DNA of known microorganisms to identify which microorganism or microorganisms are present in the sample. Identification is also made of specific genes associated with, for example, antibiotic resistance and virulence.
4. Analysis and interpretation
   A team of researchers is working together to interpret the meaning of the microorganisms and genes identified in the sample. The effect of the variants, i.e. deviations from the reference genome, that occur is studied in detail. The team uses different programs and resources depending on the specific question to be answered, such as genetic databases, our own research and literature.
5. Results
   A report describing the findings of the DNA sequencing is produced. If necessary, an oral presentation of results is also carried out to facilitate decision-making.

Deliveries

The results are summarized in a report and presented orally to the customer.