Katerina Efthymiou

PhD, Senior Scientist, R&D, Digital Innovation, NextGen Sequencing, Chr. Hansen

Boosting efficiency, capacity and scope: Insights from high-throughput sequencing in Chr. Hansen

Second and third generation sequencing platforms are part of our core sequencing facilities to generate high-quality sequencing and catalogue the genomic signature of each strain present in the Chr. Hansen Culture Collection. This information is crucial in various and diverse applications, from in silico screening and strain selection for culture designing, to strain identification, safety assessment and mode of action studies.

We focus on workflow automation and process optimization to reduce costs, decrease lead time, improve efficiency and data quality; owing to this approach we were able to increase the sequencing capacity of our Illumina shotgun sequencing workflow to 96 samples. Detailed changes throughout the workflow, such as the replacement of the chemistry in the DNA extraction and library preparation with cheaper & faster alternatives and the miniaturization of the reaction volumes in library preparation, allowed us to reduce the cost by 1 million dkk annually. Implementing Oxford Nanopore Technologies (ONT) sequencing allows for further optimization, due to cheaper consumables, simpler and more efficient workflows, and plastic waste reduction and development of novel applications. Meanwhile, improved data quality is achieved by overcoming assembly challenges (due to e.g., genomic repeats), sequencing-technology bias, providing a perfect genomic signature of each of our strains.