STSM - How I discovered the world of bioinformatics.

My name is Stefanie Engelke and my PhD project at Leibniz Institute for Farm Animal Biology (FBN) (Dummerstorf, Germany) is dealing with the level of methane output of dairy cows and the aim to validate an indirect marker to quantify methane emission based on milk fatty acids feeding different diets. Both, milk fatty acid composition and methane production depend on rumen metabolism, which is shaped by the microbial population. That was the starting point of my journey into a new field because I wanted to know more about the relationships, coherent pathways and involved teammates creating the differences. Thanks to the sponsorship by the METHAGENE COST Action STSM, I could follow my curiosity and thirst of knowledge. DNA from rumen microbial samples of my PhD-project were analyzed for bacterial and archaea gene sequence before my arrival at the research team of Dr. Diego Morgavi at UMRH (INRA ARA, Saint-Genès-Champanelle, France). There, I had the opportunity to have a knowledgeable and detailed guidance by Dr. Milka Popova and Aurélien Bernard during the challenges of processing the enormous raw data set generated by next-generation sequencing method.
During my stay I learned to process 16S rRNA gene sequences using the mothur software that included working on quality filtering, OTU picking, taxonomic assignment, phylogenetic reconstruction, diversity analyses and visualizations for overlapped reads. Any time I could ask and discuss emerging problems with the experts at the research team DINAMIC which is not to be taken for granted. I am looking forward to use the obtained DNA data and integrate the microbial information in the interpretation of my project results. It was the first time that I worked with DNA sequence analysis and in the end of this internship, I could say that I extended my knowledge and faced the challenges that are emerging when working with DNA sequencing data. There was also time for visiting a cattle farm of INRA and see their GreenFeed system as well as some preparations for future SF6 measurements. Furthermore, I met other young researchers from different countries at UMRH and it was a pleasure to spend time with them and talk about their experiences, projects and much more! Thanks to all of you and as well to my supervisors Dr. Cornelia C. Metges and Dr. Bjõrn Kuhla who are supporting me. It was a great time!