Research Group Microbial Genomics

Our research group focuses on Food Safety and Strain Discovery within the context of health and biodiversity. To achieve this, we primarily apply molecular microbiological techniques and DNA sequencing of microorganisms. The analysis of sequence data and the development of dedicated tools are carried out in close collaboration with the Bioinformatics department. In education, Biology and Medical Laboratory Research students are encouraged to conduct complex data analyses using accessible bioinformatics tools on the Galaxy platform alongside their laboratory work.

stagiair voert handelingen uit op het DNA lab

In the LCAB laboratory, we carry out molecular microbiological research and make extensive use of DNA sequencing technologies. Methods for applying both Whole Genome Sequencing (WGS) and Metagenomics Sequencing are continuously optimized, and relevant quality controls are performed to generate high-quality sequence data. Together with the Bioinformatics department, we develop accessible data analysis tools, pipelines, and web applications that are used by both our team and industry partners for data analysis.

Nanopore sequencing plays a central role in our research. Because we work with diverse samples (such as milk, chocolate, meat, and rinse water) and various bacterial species (Listeria, Salmonella, E. coli, Lactobacillus), optimizing DNA isolation protocols is frequently required. Furthermore, we recently developed a method to apply WGS to very low DNA concentrations. This approach enables us, for example, to detect low levels of pathogens in food products and manufacturing facilities.

We will soon begin setting up a Strain Discovery platform. There is high industry demand for natural microbial strains for various applications, including food production, pharmaceuticals, and biotechnology. By combining selective sampling, selective culturing, machine learning, and Next-Generation Sequencing (NGS), we actively search for microbial species with specific functional properties.

Students completing an internship with our research group gain extensive hands-on experience with Nanopore technology, related molecular microbiological techniques, and data analysis. This thoroughly prepares them for the professional field, where sequencing technologies are increasingly applied.

The growing use of sequencing technologies yields larger volumes of data, increasing the need for bioinformatic data analysis. We aim to address this need and strengthen the bioinformatic skills and knowledge of students enrolled in the Biology and Medical Laboratory Research program. Data analysis methods are developed in collaboration with the Bioinformatics department.

Contract Research

The LCAB offers contract research to an increasing number of companies and possesses a broad range of advanced analytical techniques to answer practical industry questions. Companies engage the LCAB for support in:

Detecting and characterizing microorganisms in water, soil, air, humans, animals, and plants.
Analyzing contamination routes within production environments.
Whole Genome Sequencing (WGS) and bioinformatics for in-depth microbial typing.
Optimization and monitoring of fermentation processes.
Data analysis and interpretation of complex microbiological datasets.

By combining practical expertise with innovative technologies, the LCAB helps companies and organizations gain insight into their products, processes, and environmental diversity, enabling targeted improvements in quality, safety, and product development.

Contact

For more information on collaborating with the Microbial Genomics research group, contact:

Dr. Astrid Heikema (Professor / Lector): [email protected]
Marijke Mostert (Project Manager): [email protected]

Key Focus Areas & Other Research

Campylobacter (One Health Approach)

Within the One Health framework, the interconnection between human, animal, and environmental health is central. This is particularly crucial for zoonotic diseases that can transfer from animals to humans, such as campylobacteriosis. While common in Europe and typically associated with poultry consumption, relatively little is known about other potential sources like dogs, despite humans having close contact with them.

In ongoing research, the LCAB analyzes samples from dogs in various settings, such as veterinary clinics and shelters. Findings show that Campylobacter occurs regularly in dogs, including Campylobacter jejuni, a bacterium that causes illness in humans. Using DNA analysis, we investigate the extent to which these bacteria match strains found in humans and other animals. Early results indicate that the majority of types found in dogs are also present in humans, suggesting dogs may play a role in spreading the bacterium.

Furthermore, we examine specific bacterial traits linked to neurological complications like Guillain-Barré syndrome.

RAAK Bieren (Beer Research - Lead: Avans University)

The Netherlands boasts a rich beer culture with hundreds of craft breweries. To give brewers and suppliers better control over the brewing process, craft breweries, suppliers, Avans University of Applied Sciences, and Hogeschool Leiden are collaborating on an innovative sensor based on near-infrared technology and machine learning to continuously monitor fermentation. Additionally, extensive yeast research is being conducted, analyzing 100 practical samples for genetic traits, flavor profiles, and haze using advanced -omics techniques and data analysis.

Featured Research Projects

STRAIN-AI: Smart Technology for Faster Microbial Innovation

An innovative research project utilizing Artificial Intelligence (AI) and advanced DNA technology to accelerate the identification of valuable microorganisms for the food industry and biological crop protection.

Advanced Precision in Food Safety (Completed)

Building on previous food safety research, focusing on Listeria monocytogenes, Salmonella, and toxin-producing E. coli to identify sources of contamination and analyze genetic traits related to virulence or environmental persistence.

Precision Food Safety (Completed)

Investigated the use of Whole Genome Sequencing (WGS) for detecting pathogenic bacteria within the production chain and transferring this knowledge to the food processing industry.

Our Professor of Applied Sciences

Dr. Astrid Heikema has been the Professor (Lector) of the Microbial Genomics research group since November 2022. Together with industry partners and students, she develops innovative applied research initiatives.

More about Astrid Heikema (in Dutch)