Fungi are popular production cell factories for metabolites, proteins and enzymes in biotech industries.  As sustainable alternatives to chemicals and conventional agro-products, fungal products have been considered a key player in transition from our petroleum-based economy into a biobased circular economy (1, 2). To promote mass production, modern biotech companies make use of targeted genome editing tools to secure, stabilize and enhance desired products (3, 4).

Project manager
June 2022 to October 2023

To guarantee the quality of improved fungal strains, genomic DNA sequencing and comparative genomics must be applied regularly to create a blueprint of the genomic lineage of the strains. However, conventional sequencing platforms can only be performed via service providers or start-up investments reaching 2 million euros. The data analysis could take as long as 6 weeks turnaround time or even longer.

Scalable toolkit

Starting from 2016, the researchers in Centre of Expertise Biobased Economy (CoE BBE) have been developing a portable sequencing system which is tailor-made to suit the needs of small and medium biotech companies (5). As a proof-of-concept pilot, The Protein Brewery (TPB) B.V. requests this expertise from CoE BBE. The purpose of this pilot project is to test and tailor the portable sequencing prototype (Oxford Nanopore Tech MinION®) with the TPB fungal production strains. If successful, the result will be a scalable toolkit which helps to promote desired fungal products with lower costs and easier viable strains.

Upgrade sequencing system

At this moment we are approaching the mid-term of the project. With the combined efforts of researcher Bazante Sanders, internship students and TBP, we managed to upgrade the sequencing system with a novel multiplexing option. Instead of one sample per round, the current system is able to handle up to 24 samples at each experiment. This decreases the cost of genomic blueprinting from ~1000€ per sample (cost March 2022) to ~60€ per sample (cost December 2022). The quality of the data was also largely improved comparing the method in 2021. Both research group Biobased Building Blocks & Products and TBP experts were satisfied with the current development. In the second half of the project we plan to test this method on several commercial strains to make highly reliable genomic “lineage certificates”.

We hope in the future we can move on with new technological developments together with a broader range of stakeholders. The outcome of our project will be a useful tool to help in bringing affordable alternative fungal products to the markets. This will eventually become a beneficial factor to increase industrial contribution to climate change mitigation in a biobased economy (2).

  1. Meyer, V. et al. Growing a circular economy with fungal biotechnology: a white paper. Fungal Biol Biotechnol 7, 5 (2020).
  2. Hyde, K.D. et al. The amazing potential of fungi: 50 ways we can exploit fungi industrially. Fungal Diversity 97, 1-136 (2019).
  3. Cerimi, K., Akkaya, K.C., Pohl, C., Schmidt, B. & Neubauer, P. Fungi as source for new bio-based materials: a patent review. Fungal Biology and Biotechnology 6, 17 (2019).
  4. Baker, S.E. Grand Challenges in Fungal Biotechnology. Frontiers in Fungal Biology 1 (2020).
  5. Jain, M., Olsen, H.E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology 17, 239 (2016).


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