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Interview: Integrating metagenomics and culturomics

This is the fifth interview with the PhD students of the Complex Systems & Metagenomics projects in a series of background articles. Keep following this website for the next interview in this series.


Interview with Simen Fredriksen, PhD candidate of the project ‘Microbiome fortification for healthier pigs through metagenomics-driven culturomics and microbial bioactive metabolite discovery’.

I chose to do a PhD in metagenomics due to having an interest in microbial ecology as well as a more general interest in science. The work I do is similar to what I did as a master student at the University of Oslo, so I knew what I was signing up for. I find microbiome research interesting in part due to it being a relatively new and fast developing field that still has many unanswered questions. Apart from the academic side, I am happy to be working on a project that has concrete goals towards improving animal and human health.

The ultimate goal of my project is to reduce the prevalence of infectious disease in pig farms. As antimicrobials have been widely used to prevent and treat infections (some of which have zoonotic potential), antimicrobial resistance has emerged. Thus, my project also impacts on the health of humans and the global one health. Methodically, my project is centered around integrating sequencing technology and bioinformatics with culturing of bacteria and other microbiological methods. Most importantly, I utilize metagenomics to detect genetic markers associated with healthy and diseased animals. These markers can be used to identify members of the microbiota which can antagonize pathogens as well as previously unknown synergies between co-infecting organisms.

The most challenging part of my position is acquiring metagenomics samples from diseased farm animals, as the window of time between the observation of relevant symptoms and antibiotic treatment can be small. Additionally, it is not always straightforward to identify what disease a pig is suffering from. The most enjoyable part of my position is working with bioinformatics on large datasets. It is also nice to be conducting multidisciplinary science in collaboration with researchers from a range of different universities and countries. Similarly, I find it important to interact with veterinarians and other members of the pig farming industry in order to properly understand my study system.

PhD project: Microbiome fortification for healthier pigs through metagenomics-driven culturomics and microbial bioactive metabolite discovery.