Matti Ruuskanen
PhD, Docent
matti.ruuskanen@utu.fi ORCID identifier: https://orcid.org/0000-0003-4221-2880 |
Microbiomes; bioinformatics; microbiology; data science
Microbiomes and health, microbiome data science
I received my MSc in Microbiology from University of Helsinki in 2014, where I studied e.g., the spread of antibiotic resistance genes during manure application. I completed my PhD research between 2015 and 2019 at University of Ottawa (Canada), where I investigated the sediment communities in Arctic lakes and how they respond to anthropogenic stresses. I started working at University of Turku in the groups of Teemu Niiranen as a postdoctoral researcher. Between 2021 and 2025 I continued my work in the group of Leo Lahti with postdoctoral funding from the Finnish Research Council and the Finnish Cultural Foundation. During my postdoc period I studied e.g., associations between incident and prevalent chronic diseases and human gut microbiomes in the FINRISK cohort. In 2023, I received the Title of Docent in Microbiology, from University of Helsinki. I have worked as an University Lecturer at the Department of Life Technologies since May, 2025.
Currently my research covers both applied microbiome data science and related method development. Many of the ongoing projects deal with functional data from metagenomics and utilization of temporal multiomics. I am specially interested in the microbial metabolism of dietary compounds and their mechanistic associations with human health and chronic diseases.
I have taught several laboratory and lecture courses as an assistant teacher at University of Helsinki and University of Ottawa (Canada) during my studies. Since 2019 I have been asked to give lectures on microbiome data science and related topics on courses at University of Helsinki, Karolinska Institutet (Sweden), Savitribai Phule Pune University (India), Universitas Gadjah Mada (Indonesia), University of Tirana (Albania). Additionally, I have organized and taught in several international workshops in Finland and in other European countries. At University of Turku, I was the main lecturer on the Machine Learning and Algorithmics course (TKO_3121) between 2021-2024.
I am currently teaching on Solu ja Biomolekyylit -teoria (BKEM5030), Elintarvikelainsäädäntö ja elintarvikevalvonta (ETEK0003), and Mikrobiologia (BKEM5013).
I have supervised 4 BSc theses, 6 MSc theses, and I am currently supervising 3 PhD researchers.
I have a docent contract with University of Helsinki and I have completed the teacher's pedagogical studies (60 ECTS).
- Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults (2022)
- Diabetes Care
(A1 Refereed original research article in a scientific journal) - Suomalaisten suolistomikrobiston koostumus on yhteydessä tyypin 2 diabeteksen riskiin (2022)
- Diabetes ja lääkäri
(D1 Article in a professional journal) - Towards standardized and reproducible research in skin microbiomes (2022)
- Environmental Microbiology
(A2 Refereed review article in a scientific journal ) - Associations of healthy food choices with gut microbiota profiles (2021)
- American Journal of Clinical Nutrition
(A1 Refereed original research article in a scientific journal) - Links between gut microbiome composition and fatty liver disease in a large population sample (2021)
- Gut Microbes
(A1 Refereed original research article in a scientific journal) - Modelling spatial patterns in host-associated microbial communities (2021)
- Environmental Microbiology
(A2 Refereed review article in a scientific journal ) - Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments (2020)
- Limnology and Oceanography
(A1 Refereed original research article in a scientific journal) - Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere (2020)
- ISME Journal
(A1 Refereed original research article in a scientific journal) - Warming climate is reducing the diversity of dominant microbes in the largest High Arctic lake (2020)
- Frontiers in microbiology
(A1 Refereed original research article in a scientific journal) - Physicochemical drivers of microbial community structure in sediments of Lake Hazen, Nunavut, Canada (2018)
- Frontiers in microbiology
(A1 Refereed original research article in a scientific journal)



