Molecular biology tools, computational food and health science

Studying complex microbial communities is a challenging task. Here at the Department of Food Science, we employ a wide range of cutting-edge tools and methods that allow us to investigate these communities and their interactions with one another and their host.

At the core of our research lies DNA sequencing technology, as genetics holds crucial information about microbial identity, their functional capabilities, and the ways they interact with their environment.

DNA sequencing has revolutionized our ability to study microorganisms—not just at the level of individual organisms, but also within complex communities and specific environments such as the human gut. This technology has enabled detailed molecular-level analyses that were previously unattainable. The advent of high-throughput sequencing methods has led to the generation of massive amounts of data, necessitating the use of advanced computational tools to extract meaningful insights.

Research Themes

 

In addition to the genetic information encoded in the DNA sequence, DNA methylation plays a pivotal role in gene regulation and in how bacteria defend themselves against phages. Epigenetics holds the key to understanding how the same genetic information can be interpreted in different ways across various bacterial species.

Our section was the first to demonstrate a cost-effective, high-precision, and scalable method for studying bacterial methylation maps using nanopore technology. This groundbreaking research has opened new avenues for discovery, allowing us to explore epigenetic modifications in ways that were previously impossible. This exciting field promises innovative applications in the development of safer, more sustainable food products.

 

In our section, we develop and utilize bioinformatics tools to analyze and interpret large-scale sequencing data. These tools are essential for tasks such as sequence alignment, genome assembly, and functional annotation, allowing us to understand the genetic and functional diversity of microbial communities. Our work integrates both established techniques and cutting-edge innovations to push the boundaries of what can be achieved with sequencing data.

One key focus of our research is the application of long-read sequencing technologies, such as Nanopore sequencing. Compared to traditional short-read sequencing, long-read sequencing offers several advantages, including: Resolving complex genomic regions, detecting structural variations, or improving genome assembly accuracy.

This technology is particularly valuable for studying organisms with highly repetitive genomes or those that are difficult to culture, providing new insights into microbial ecology and evolution.

 

 

In addition to bioinformatics, biostatistics plays a crucial role in our research, particularly in integrating sequencing data with phenotypic data. Biostatistical methods help us: manage covariance structures, account for phylogenetic relationships, and conduct rigorous statistical analyses.

This integrative approach enables us to correlate genetic variations with phenotypic traits, providing deeper insights into the functional implications of genetic diversity.

Our goal is to develop robust computational frameworks that can handle the complexity and scale of modern biological data. By combining cutting-edge sequencing technologies with sophisticated bioinformatic and biostatistical analyses, we aim to advance our understanding of microbial ecology, evolution, and their interactions within food systems and human health.