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).
- Lifestyle associates with unique resistome and microbiome signatures in children (2026)
- BMC MicrobiologyBriefings in Bioinformatics
(A1 Refereed original research article in a scientific journal) - Multi-omics time-series analysis in microbiome research: a systematic review (2025)
(A1 Refereed original research article in a scientific journal) - Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals (2025)
- Microbial genomics
(A1 Refereed original research article in a scientific journal) - Value of Multiomics Over Clinical Risk Factors in Hypertension PredictionVariation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort (2025)
- HypertensionNature Aging
(A1 Refereed original research article in a scientific journal) - (2025)
- Nature Communications
(A1 Refereed original research article in a scientific journal) - Integration of polygenic and gut metagenomic risk prediction for common diseases (2024)
- Role of Gut Microbiota in Statin-Associated New-Onset Diabetes—a Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort2024
- Arteriosclerosis, Thrombosis, and Vascular BiologyJournal of Hypertension
(A1 Refereed original research article in a scientific journal) - Comprehensive biomarker profiling of hypertension in 36 985 Finnish individualsCOMPREHENSIVE BIOMARKER PROFILING OF HYPERTENSION IN 36,985 FINNISH INDIVIDUALS (2022)
(A1 Refereed original research article in a scientific journal) - (2022)
- Journal of Hypertension
(Other publication) - Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting (2022)
- Cell Metabolism
(A1 Refereed original research article in a scientific journal)



