Using DNA sequencing and bioinformatics, microorganisms and microbiota can be identified and characterized with high precision in products, processes, clinical and biological samples, as well as in the environment. We support all stages of your sequencing project—from experimental design to translating complex sequencing data into decision-making.

DNA is the foundation of most microbial biology, making sequencing a powerful tool with many applications. It can be used to trace microbial contamination in production facilities, analyze microbiota composition in clinical samples, identify infection biomarkers and vaccine candidates, or detect resistance genes in isolated bacteria. Beyond harmful microbes, we also work with beneficial microorganisms in products, processes, microbiota, or the environment (e.g., food production microbes or bacteria that degrade persistent compounds). For example, we can monitor microbiota changes during fermentation or product storage.

A key advantage of sequencing is the ability to analyze the entire microbiome—not just cultivable organisms.

How RISE can support your sequencing project?

We conduct sequencing projects involving viruses, bacteria, yeasts, and molds, as well as antimicrobial resistance and other traits. Our expertise spans sampling and DNA extraction from complex samples, with deep understanding of customer needs. Our knowledge is built through in-house research and close collaboration with industry in applied and contract research.

We can also complement genomics or metagenomics with other omics approaches (e.g., transcriptomics, proteomics) to gain deeper insights. Multi-omics enables solving complex problems previously out of reach, especially when integrated using advanced data analysis and AI.

We offer full or partial project support, including:

• Study design and planning: methodology, sampling strategy, sequencing technique selection, and analysis planning.
• Sampling from complex environments, products, and biological materials.
• Sample preparation and DNA extraction in Bio Safety Level 2 (BSL2) labs.
• Sequencing using short-read (e.g., Illumina) and long-read (e.g., Oxford Nanopore) technologies:
  • Whole genome sequencing of bacterial isolates for identification, outbreak tracing, resistance gene detection, virulence markers, novel functions, etc.
  • Amplicon sequencing (e.g., 16S rRNA, ITS) for microbiota composition analysis.
  • Shotgun metagenomics for characterizing unknown microorganisms and microbiota.
• Bioinformatics analysis (e.g., strain comparison, SNP analysis, MLST, cgMLST, genome assembly from metagenomes) for product development, quality control, benchmarking, outbreak tracing, microbiome profiling, biomarker discovery, etc.
• AI-driven integration of genomics/metagenomics with other omics data for interpretation and decision support.
• Customized training

We use modern high-throughput sequencing technologies, including Next-Generation Sequencing (NGS, e.g., Illumina) and third-generation sequencing (e.g., Oxford Nanopore). Depending on project needs, we apply and adapt microbiological methods from sampling and DNA extraction to sequencing and data interpretation.

We can also integrate other omics methods such as transcriptomics, proteomics, metabolomics, glycomics, and lipidomics.

Project overview DNA sequencing

1. Sample collection
   Representative samples are collected from products, processes, clinical materials, or environments. Microorganisms are isolated or microbial DNA is extracted, purified, and quality-checked.
2. Library preparation and sequencing
   Extracted DNA is prepared for sequencing and processed in sequencing instruments that read the DNA sequence.
3. Bioinformatics
   Powerful computing tools filter and analyze the large volumes of sequencing data. Genomes are reconstructed and compared to reference databases (e.g., ENA, GenBank) to identify organisms and genes of interest (e.g., resistance, virulence).
4. Analysis and interpretation
   Our research team interprets the findings, studying genetic variants and their implications using databases, literature, and custom scripts tailored to the project.
5. Results
   A report is produced summarizing the sequencing findings and analyses. If needed, we also provide oral presentations to support decision-making.

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

Many processes and production environments must be clean and hygienic for the product to be safe and durable. It is also important that process steps and equipment designed to reduce unwanted microorganisms function properly. RISE offers a number of services and tools to improve microbiological safety and dureability.

Microbiological risk assessment combined with mathematical modeling of growth and killing / inactivation at varying physical conditions, for example different temperatures and pH are useful tools in product development or suspicion of microbiological contamination of a manufacturing process.

We carry out assignments concerning disease-causing and spoilage (product-detroying) microorganisms (viruses, bacteria, yeast and mold), as well as antimicrobial resistance. Our practical and theoretical knowledge has been built up through our own research and in close collaboration with industry in applied research and commissioned projects.

The results from risk assessments are useful in, for example, the development of a new product in order to be able to assess whether the production process is safe. Another area of use is when a company wants to identify preventive measures to avoid the spread of disease-causing or spoilage  microorganisms.

RISE performs both theoretical and practical microbiological risk assessments. For the risk assessments that contain experiments, we use RISE well-equipped microbiological laboratories where we have the opportunity to work with disease-causing microorganisms in the projects where there is a need for this. We also have the opportunity to do field experiments at our customer´s production sites to collect data and observations that can form the basis for the risk assessment.

We offer you as a customer to work with us on issues around:

• Troubleshooting of microbiological problems and transmission routes of microorganisms.
• Risk assessment and modeling - theoretical assessment of the conditions for relevant microorganisms for growth, inactivation and / or survival.
• Isolation and identification of microorganisms in a product, ingredients, material or production facility.
• Shelf life test / storage studies of existing products to answer how long the product can be stored.
• Challenge test - bacteria, viruses, yeast and / or mold are added to the product to evaluate whether it is microbiologically safe and shelf-stable.
• Product development - How do the properties of the intended product affect the microbiological quality?
• Production side streams - How can they be made microbiologically safe and stable?
• Hurdle technology - How to combine different factors such as temperature, pH, preservatives, etc. to obtain a safe product with good microbiological quality?
• Advice on preservatives - Which ones are appropriate and what does the legislation say?
• Consulting in environmental monitoring according to FSSC 22000 2.5.7

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

Files to download:

Relevant standards

Past and running projects within RISE

We offer the possibility to compare the effect of your current cleaning and disinfection with new alternatives.

This is a service provided by the RISE test bed Cleaning Innovation.

New technique intended for cleaning and disinfection is continiously developed. But how can a food manufacturer evaluate a new concept without disturbing the production? How can the company be assured that the new technique is as good as or better then their current technique?

In Cleaning Innovation we offer the possibility to perform a two-step independent evaluation and comparision. The result from the study will be a good decision basis for a safer and easier change of technique

Step 1- Gathering of facts and evaluation in model system

Micro organisms from the current production lines is collected as well as data from the companys cleaning control. The information is used to design the model system where the initial evalutation will take place. We identify the demands that have to be fulfilled for the alternative technique to be regarded as good enough. The following factors can be adapted: choice of technique, chemicals, time, temperature, material, soil and micro organsims (pathogens and spoilage flora).

Step 2 - Control and follow up

Given that the efficiency criteria for pass have been fulfilled using the model system in lab/pilotscale a control and follow up of the effect, in full scale at your site, is offered. Sampling of microorganisms on surfaces (swabs for total number, Enterobacteriaceae, yeast or specific pathogenes) and/or in air. Residues of soil on surfaces (ATP, protein) is also gathered and analysed. The samplig is done after the current cleaning/ disinfection procedure and is repeated after having used the alternative technique for a numberof weeks/months.

Results and conclusions are compiled in a report that is presented at a meeting.

Delivery time depends on the complexity of the project.

If a process equipment is easily cleaned it will be a big advantage when assuring a hygienic production and minimizing the total cost for use. Getting the equipment clean is as vital as making sure that the cleaning process is not too time consuming.

This is a service provided by the RISE test bed Cleaning Innovation.

Product contact surface - open cleaning or closed (CIP)

In the testbed Cleaning Innovation we can measure and evaluate how much product residues and/or micro organisms that are left after cleaning, disinfection and/or sterilization.

Non product contact surface - outside equipment

Contamination gathering on the outside of the equipment will soon be a quality problem. Cleaning Innovation provides possibilities to evaluate cleanability of the outside of theequipment in our pilot plant.

We offer among others the following services in laboratory or pilot/full scale:

• Analysis of microbiological cleanliness
• Test of how the material effects the cleaning result
• Evaluation of cleanability using model soil
• Detection and characterisation of residues of soil, allergens and chemicals

Validation of CIP and other cleaning routines.

Highly skilled employees are needed in order to meet today's demands for quality assured cleaning of food premises out of an environmental point of view, as well as to maintain product safety. We offer theoretical and practial training sessions on cleaning for food companies.

This is a service provided by the RISE test bed Cleaning Innovation.

After the training session the employees will be able to:

• Understand the consequences of improper cleaning.
• Recognize factors impacting the cleaning result.
• Perform efficient cleaning based on hygiene plans and instructions.
• Control the results of their own cleaning.
• Understand the cleaning's effects on environment, and know how to minimize these.
• Handle chemicals and equipment in a safe manner.
• Understand how costs can be reduced with efficiency and preserved quality.
• Minimize the risk of interruptions in the manufacturing process as a result of faulty cleaning.

Cleaning Innovation wants to increase the level and the pride of active cleaners with this education.

The importance of good cleaning and industry requirements in the food industry are the goals!

Participants will recieve diplomas in the form of a course certificate.