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Welcome: Alexandra Koumoutsi
New Head of Microbial Automation and Culturomics Core Facility discusses her career and goals for the facility’s future
Hailing from the sunny shores of Volos, Greece, Alexandra Koumoutsi has had a career spanning continents and organisms. She recently stepped into a new role as the Head of the Microbial Automation and Culturomics Core Facility at EMBL Heidelberg. We had the chance to catch up with Koumoutsi about her plans for the new facility, her academic background, and how she recharges herself when she is out of the lab.
Tell us a bit about your academic and professional background.
I initially studied chemistry/biochemistry at the Aristotle University of Thessaloniki. While I really like chemistry, I became particularly curious to learn how it directs biological processes in living organisms. So I moved to Berlin, where I did my PhD at the Humboldt University on functional genomics, studying Gram+ soil Bacilli and fungi. Fascinated by microbial interactions, I moved to the University of California, San Francisco for my post-doctoral studies, to further broaden my horizons in host-pathogen interactions. Initially, I studied biofilm formation in a comparative genomics fashion, using Yersinia bacteria and the nematode C. elegans. Further on, using high-throughput genetics and phenotyping, I systematically probed interspecies interactions between the pathobiont C. albicans and bacteria it encounters in vivo. I continued this line of research as a postdoc in the Genome Biology Unit at EMBL. Together with collaborators, I expanded in this direction to set up strain collections, study the E. coli pangenome (genotype-phenotype associations) and establish new methods to construct and deconvolute genome-wide mutant libraries in different bacteria. I used these tools to dissect intra- and interspecies interactions. At the beginning of May, I started at this new EMBL core facility. I want to contribute with my expertise in genetics, microbiology, systems biology approaches, and automation.
What technologies will the Microbial Automation and Culturomics Core Facility provide access to and what sort of new science do you think it will help enable?
At EMBL, there is already broad interest in microbial research, with the current program touching upon microbes and their communities from different angles: microbiomes in humans, pathogens during infection, or environmental communities.
The facility will give researchers access to and training in cutting-edge equipment that will expedite their work on microbes and microbial communities. Importantly, the entire facility is in a biosafety level 2 setting and has automated systems within controlled environments, such as anaerobic chambers. The users will be able to do high-throughput cultivation of different species, strain collections, and communities. Moreover, we’ll train users on how to design, create, and use genome-wide genetic tools. Genetics is the basis for dissecting the molecular functions and interactions of these microbes. Finally, we’ll train and assist users with high-throughput phenotyping. The facility is equipped with automated platforms: liquid handlers, integrated platforms, and colony picking and pinning robots necessary for probing large numbers of microbes, communities or mutants with quantitative readouts.
There is already expertise across different groups of EMBL’s Microbial Ecosystems Transversal Theme, which we will bring into the facility. Unique know-how, resources, and tools that are currently pioneered at EMBL will be disseminated to the entire scientific community.
As the leader of this new facility, what are your priorities going forward?
The priority is to get all equipment set up, and train the hired personnel, as we aim to open up for users in spring 2025. We reached out and will continue to connect with researchers and core facilities within and outside of EMBL to understand user needs, and synergies, and explore technologies we should bring/develop here.
When did you first decide that you wanted to be a scientist?
I discovered science in high school when I realised how fascinating our environment is – how plants, animals and people grow and change. This interest in nature is what brought me to science, initially, and I continued it by studying chemistry at university.
How do you recharge yourself when work gets chaotic?
I walk a lot and I play board games with my children. I love being outdoors, and the forests around Heidelberg offer a good opportunity to do this.
If you couldn’t be a scientist, what other career might you have pursued?
That’s a tough one. I would love to be in the music business [laughs], but I am very untalented in that area. I used to play an instrument as a child, but I haven’t in many years.
Which book or movie are you most likely to recommend?
I have many favourite books, but recently, I read The Prophet Song, by David Lynch. That’s a book I would recommend to people – it’s a difficult read, but I think it is eye-opening.
As EMBL recently celebrated its 50th anniversary, we’re asking colleagues if they have any birthday wishes for EMBL…What is yours?
My wish is for EMBL to stay as innovative and forward-looking as it has always been, so it will continue to be a beacon for molecular biology research worldwide.
