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- Thijs Ettema
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I am interested in microbial evolution. I find it fascinating that microbes have been on Earth long before us and play such an important role, both in our everyday life and on the large scale in the environment, health, industry. Although invisible to the naked eye, we are nowadays equipped to zoom into their world with unprecedented capabilities. Recent development of methods to study environmental microbes, such as metagenomics and single cell genomics, inspire my research. There is yet quite some exploratory effort before we can fully appreciate the diversity of the microbial world and its most interesting aspect, to me, is the dynamics of how things change.
By family tradition I have spent most of my early years of education on mathematics, in particular four years of a high school. Biology fascinated me and I became interested in the intersections between mathematics and biology. In school biology teacher inspired me to work on a predator-prey model based on excellent ecological data on wolves and lynxes from Bialoweza forest (special award in 13th European Union Contest for Young Scientists, Bergen 2001). As an undergraduate I continued with mathematics focusing on probability and its applications in biology (Bachelor degree in mathematics, Warsaw University, 2004). Following my biological interest, I then switch to molecular biology (Bachelor degree in molecular biology, Warsaw University, 2005), enjoying genetics the most, and finally discovering bioinformatics (Masters of science in biology, Uppsala University, 2007).
During studies in Uppsala I got inspired to use bioinformatic methods in the studies of bacterial evolution and I joined the lab of Prof Siv Andersson, who was my phd supervisor. I was excited about the new developments allowing insights into the unknown environmental microbes. My first project was analysis of bacteria from a Neanderthal bone sample and I also looked into Ötzi’s gut sample, trying to understand what could have shaped the communities found there. Ancient datasets are scarce, comparisons are difficult and understanding the microbiology of the unique taphonomic histories of different samples remains an exciting challenge. I also studied lake bacteria from Swedish and American lakes. Already early on it became obvious that analysis of the mix of organism in the metagenome has certain limitations. I was very excited to observe the development of single cell genomics, that I consider an excellent complementary approach, and lucky to be involved in a collaboration that aimed at obtaining single bacterial cells from lakes. My single cell project focused on one particular freshwater bacterium, which show some striking differences compared to its closely related common oceanic bacterial ‘sister’. In practice, what I enjoy doing on a daily basis is large scale next-generation sequencing data analysis.
I continue working with metagenomics and single cell genomics on a post-doctoral position I started in November in the Ettema-Lab.