iOMEGA project: one year and beyond

Around this time in 2018 the iOMEGA (integrated omics for metabolome and genome annotation) started. In the picture above new PIs and postdocs are happily celebrating the start of the granted projects by slicing a large piece of cake. We also pitched the projects explained the biological challenges we would tackle using eScience solutions. In my project the daunting task is to find relevant and useful correlations between genomics and metabolomics data to assist in the structural elucidation of natural products. These structurally very diverse molecules have inspired high-value applications like antibiotics and therapeutics. Currently, there is a lack of novel antibiotics to combat resistant bacteria. Nowadays, we can collect increasing amounts of genomics data including information on which genomes and genes are present in soil, on plants, or in cultures; and also increasing amounts of metabolomics data that include information on which molecules are present.

All of this provides us with a potential goldmine of structurally novel molecules never seen before by the resistant bacteria. However, to effectively mine these daunting data sets, novel computational solutions are needed to i) finding novel chemistry and ii) structurally elucidate the molecules using information from both the genes and the metabolomics data. For example, in metabolomics data all the molecules are represented by spectra from which we still need to puzzle or infer the actual structures of the measured molecules. In the picture below, I am convincing the audience during the celebration day that we have many things in place but still lack parts of the workflow to more effectively integrate genomics and metabolomics data to accelerate elucidation of natural products. So I was eager to start with eScienceCenter engineers to start putting things in place!

Fast forward one year and the iOMEGA project is in full swing! With three eScienceCenter engineers, a postdoc, and MSc students involved, I have grown in my role to lead a team of scientists to collectively work on one goal within the different projects. Each month we have a project meeting were we share the progress and discuss the choices we have to make. One of the main projects we currently work on are to find a solution to more efficiently capture so called paired omics data sets where genomics and metabolomics data is obtained for the same sample. Another project focuses on how we can better assess novelty by better assessing similarity of molecular spectra or similarity of clusters of biosynthesis genes that encode for the natural products. Finally, we are also working towards a large collection of substructures that we can recognize in mass spectrometry-based metabolomics data. Below, you see a picture where I present our first paper from the project that enabled us to more quickly get a grip on what kind of molecular substructures can be identified in metabolomics data. This was part of a talk with Dr. Florian Huber, one of the eScienceCenter engineers working with me, where we explained how we applied different natural language processing algorithms to further a completely different scientific domain, namely omics sciences.

The work on the above picture I will also present in Edinburgh where Dr Simon Rogers and myself will also discuss the paper with other experts in the field as part of the famous long-standing Faraday Discussions being held in the UK. There is a nice video on these meetings available where the concept is explained. I look forward to brainstorm on how to take substructure-based deciphering of complex metabolite mixtures further. During the large Metabolomics2019 meeting in The Hague, NL, in June this year we are organising a workshop to discuss the different aspects of linking genomics and metabolomics data. This is the right place to also acknowledge all my collaborators in different labs in the UK, Denmark, and USA to work with me on these fascinating subjects.

I excited to see what the future brings and hopeful that our tools will contribute to get a more comprehensive and detailed picture on the molecular diversity produced by bacteria, fungi, and plants around us. I am keen on taking the challenge to come up with novel solutions and platforms to study these fascinating molecules! Please get in touch if you have any ideas to drive my research forward or if you like to try the tools that we are developing.