Bring light into the dark: My lab visit to Boston
I was given the very particular opportunity to travel to the U.S. for an extended period to do a lab visit in the group of Curtis Huttenhower at the Harvard T.H. Chan School of Public Health. I was there from June to July, so I was able to enjoy the wonderful summer season in Boston.
Here in the research group, I have been involved with a project to identify all gene products in the metagenome data from the Integrative Human Microbiome Project (HMP2 or iHMP) Inflammatory Bowel Disease Multi’omics Database (IBDMDB). Because even though there has been extensive research in the microbiome for a long time, there is still a large proportion of genes whose exact function is as of yet unknown. Here, I worked with the outputs of the bioinformatics pipeline Metawibele. This systematically annotates all predicted gene products in the combined microbiome of all IBD patients within the cohort using protein databases. Still unknown products are further annotated by structure prediction tools to predict the possible location within the cells and interactions with other proteins. Another function is to prioritize gene products based on prevalence and presence in microbiome dysbiosis within IBD. Therefore, important insights can be gained here as to which genes and proteins should be later addressed in the laboratory to further characterize the dysbiosis state in IBD.
In meetings with other subgroups in the working group, I got an impression of the areas in which interesting findings are being made, for example in the microbiome of domestic animals. But also, how research is practiced at Harvard and how the doctoral students there can apply for research funding to pursue a career in research in the U. S.
Boston is a city with a rich history and cultural significance. From the witnesses of the first settlement of America to the time of the American revolution, there are many attractions to visit. I was able to visit not only the Freedom Trail, which leads across the Bostonian city center, but also the sailing ship USS Constitution, which is almost as old as the U.S. itself and is still in service. I also visited many museums about human history, nature and art, which can be found across the city.
After my return, I am very happy that I got this experience of working in another work group that has different structures and work processes and therefore sometimes approaches problems differently. So, I was able to take with me the knowledge of one possible way of how to approach the problem of unknown matter within microbiome data, which will be very useful for my further work.