The human gut houses a microscopic world populated with trillions of microorganisms. This complex ecosystem, called the gut microbiome, may hold important clues about our health - past, present and future. If researchers can interpret these clues and harness the microbiome's predictive power, one day we may be able to anticipate certain illnesses before they occur - and possibly even prevent them altogether.
There are already various methods developed for disease risk prediction, with the polygenic risk score touted as one of the most promising. This combines information from multiple genetic variants in someone’s DNA to estimate their genetic predisposition to a specific trait or condition, explains Pande Putu Erawijantari, a postdoctoral researcher at the Turku Collegium for Science, Medicine, and Technology at the University of Turku. Studies have cast doubt on their usefulness however. Pande is therefore working to decode the clues lying in our gut microbiome, to add another, more dynamic source of predictive medicine to our toolkit. “Your DNA is generally stable,” she says, so there’s limited things you can do to alter the genes that may affect your risk of developing certain diseases in the future. “By using another proxy like the gut microbiome, we hope to be able to see the dynamic aspects and potentially suggest changes that can have a positive impact, like your diet, lifestyle, or medicines.”
Pande works with an interdisciplinary team at the university in the southwest of Finland, with the specific goal of establishing frameworks to understand the roles of gut microbe communities in long-term health. She has already published work on incidence of disease models to predict type two diabetes and a preprint on heart failure. To conduct this work, her team has access to health data from the FINRISK study, a large prospective cohort of Finnish adult individuals hosted by the Finnish Institute for Health and Welfare, which tracked participants from 2002 onward. They isolate DNA from the participants’ faecal samples, characterise the composition of the microorganisms, and then link this information to the decades-long health records to see what patterns emerge. The fact the research is based on faecal samples, which are non-invasive samples, means researchers like Pande have a treasure-trove of data to work with. If they can see certain signatures in the biome are predictors of health conditions in the future, experts might be able to provide suggestions for altering the makeup of the microbiome to reduce risk and improve health.
It’s challenging to model the data from the gut though, and Pande explains that currently it remains difficult to predict disease from the microbiome alone. That’s because the data is complex and “high dimensional”, meaning there are so many variables it's hard to spot patterns. To overcome this, she’s using data analysis skills, as well as machine learning, as she works to build models that can decipher the biome. The University of Turku couldn’t be better positioned for this sort of work, says Pande. Firstly, “Finland is one of the hotspots for learning about population data”, thanks to its comprehensive health registry, which researchers can access. “Then the University of Turku has hosted several population-level studies and microbiome research, so there's a lot of leading scientists already doing these kinds of projects,” she adds. Based in the department of computing for her data analysis work, Pande benefits from the multidisciplinary collaboration available at the university. This includes working closely with the faculty of medicine for the clinical interpretation of her data, as well as well-established international collaboration.
Pande has been working on the gut microbiome since her PhD at the Tokyo Institute of Technology in Japan. She further highlights her postdoctoral scheme at the University of Turku, which is run through the Turku Collegium for Science, Medicine, and Technology. “I think this is a very unique postdoctoral scheme because it's a collegium and it emphasises the multidisciplinary aspects of the research. It offers three years of funding, with a lot of self-development programmes.” She explains how the collegium organises various meetings between the groups, where they can share their research progress, and learn from different disciplines. “For example, just a few weeks ago, we got this training for the spread of science popularisation, how to write articles to reach a wider audience, and we have this blog where we can post our ideas, our thoughts on our research, or what's happening now. The collegia researchers are also actively involved in public lecture series. So I think it's very good practice as well, as a scientist, to also deliver our ideas to the public.”
The University of Turku isn’t just uniquely positioned for cutting-edge research. Pande explains it’s also an attractive destination for international researchers, who are provided with “a wide range of training”, from how to write a successful research grant, to career mentoring programmes, to pedagogy training, even to learning Finnish. The University of Turku's International Staff Services team provides information and advice to researchers moving from abroad. As an employer University of Turku invests in work well-being and promotes work-life balance through diverse services. For those with families, Pande highlights that Finland offers a good amount of support. Turku is also the oldest city in Finland, so there’s endless history and culture to explore, and it sits on the Baltic coast, at the perfect entry point to start exploring one of the world’s largest archipelagos of more than 50,000 islands.
Dr. Pande Putu Erawijantari is a postdoctoral researcher at the Turku Collegium for Science, Medicine, and Technology at the University of Turku. She currently works with an interdisciplinary team with the specific goal of establishing frameworks to understand the roles of gut microbe communities in long-term health.