The research performed in this PhD will focus on the sustainable and microbial production of specialty carbohydrates useful in human and animal welfare as well as in the agro-industry. Currently these specialty carbohydrates are produced inefficiently through complex chemical synthesis or extraction. This PhD therefore aims to reinvigorate the interest in these compounds by providing a sustainable and scalable alternative through microbial fermentation as well as by thoroughly analyzing their application potential.

In the past, these specialty carbohydrates were often discovered in plants extracts or traditional medicine but are currently little investigated with regard to their microbial natural sources. Therefore, in this project, the microbial biosynthesis blueprints will be sought after and unraveled with advanced bioinformatics tools and high-throughput screening based on functionality. The genomic DNA of various microbial strains will be extracted and subjected to third generation sequencing, allowing reliable and in-depth genome mining through public and in-house bioinformatic tools. In parallel, genomic libraries will be created from the isolated DNA and subjected to a fast and accurate metabolomic screening. Together, these approaches will enable the identification of the specific genomic sequences leading to the production of these carbohydrates.

Once the genomic blueprints have been uncovered, platform microbial production strains will be created through synthetic biology and metabolic engineering. These platform strains will be built in a plug-and-play fashion to create a flexible and versatile microbial platform technology that decreases development time of novel compounds. Construction of the metabolic pathways will occur with state-of-the-art cloning technologies such as Golden Gate and Gibson assembly while several transformation methods will be evaluated pertaining their introduction into heterologous expression hosts. The latter will be selected based on the tractability and the metabolic profile of these microorganisms. Finally, different platform strains will be combined to establish the entire biochemical synthesis pathway of one or more specialty carbohydrates, thereby yielding microbial cell factories. These cell factories will then be engineered to allow industrial manufacturing as well as compound purification from the fermentation broth.