Latest papers

Existing food processing classifications overlook the phytochemical composition

Raita, J., Ahmed, H., Chen, K., Houttu, V., Haikonen, R., Kårlund, A., Kortesniemi, M., Yang, B., Koistinen, V., & Hanhineva, K. (2025). Existing food processing classifications overlook the phytochemical composition of processed plant-based protein-rich foods. Nat Food 6, 503–512 (2025). Open-access paper. 

Plasma metabolites related to diet and microbiota may be future targets in the management of AUD

Leclercq, S., Ahmed, H., Amadieu, C., Petit, G., Koistinen, V., Leyrolle, Q., … & Delzenne, N. (2024). Blood metabolomic profiling reveals new targets in the management of psychological symptoms associated with severe alcohol use disorder. eLife Nov 29:13:RP96937. Open-access paper.

The PANIC study on the metabolic impact of diet and physical activity in adolescents

Zarei, I., Eloranta, A. M., Klåvus,  A., Väistö, J., Lehtonen, M., Mikkonen, S., … & Lakka, T. A.  (2024). Eight-year Diet and Physical Activity Intervention Affects Serum Metabolites during Childhood & Adolescence: A Nonrandomized Controlled Trial. iScience, 27(7), 110295. Open-access paper.

The GrainMark study: the impact of varying levels of whole-grain intake on the blood metabolome

Koistinen, V. M., Haldar, S.,  Tuomainen, M., Lehtonen, M., Klåvus, A., Draper, J., … &  Hanhineva, K. (2024). Metabolic changes in response to varying whole-grain wheat and rye intake. npj Science of Food, 8(1), 8. Open-access paper.

Metabolic changes in serum after a cold stimulation of brown adipose tissue

Mueez, U. D., de Mello, V. D.,  Tuomainen, M., Raiko, J., Niemi, T., Fromme, T., … & Virtanen, K.  A. (2023). Cold-stimulated brown adipose tissue activation is related to changes in serum metabolites relevant to NAD+ metabolism in humans. Cell Reports, 42(9). Open-access paper.

Advances in nutritional metabolomics related to clinical studies, microbiota and precision nutrition

Kortesniemi, M., Noerman, S., Kårlund,  A., Raita, J., Meuronen, T., Koistinen, V., … & Hanhineva, K.  (2023). Nutritional metabolomics: Recent developments and future needs. Current Opinion in Chemical Biology, 77, 102400. Open-access paper.

Review: the role of indolepropionic acid in metabolic diseases

Tuomainen, M., Uusitupa, M., Männistö,  V., Lindström, J., Tuomilehto, J., & Hanhineva, K. (2024).  Suolistomikrobiston syntetisoima indolipropionihappo metabolisissa sairauksissa. Duodecim, 140(18), 1506-1514. Open-access paper in Finnish.

Comment: Towards a harmonized metabolite nomenclature

Koistinen, V., Kärkkäinen, O., Keski-Rahkonen, P., Tsugawa, H.,  Scalbert, A., Arita, M., Wishart, D., & Hanhineva, K. (2023). Towards a  Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature. Nature Metabolism, 1-4. PDF available on request from the corresponding author.

2019–2022

The complex roles of microbial metabolites in the gut–brain axis

Ahmed, H., Leyrolle, Q., Koistinen,  V., Kärkkäinen, O., Layé, S., Delzenne, N., & Hanhineva, K. (2022).  Microbiota-derived metabolites as drivers of gut–brain communication. Gut microbes, 14(1), 2102878. Open-access paper.

5-Aminovaleric acid betaine in health and disease

Haikonen, R., Kärkkäinen, O., Koistinen, V. M., Hanhineva, K. (2022). Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease. Trends in Endocrinology & Metabolism, 33(7), 463-480. Open-access paper.

The impact of gut microbiota on mouse tissue metabolome

Zarei, I., Koistinen, V. M., Kokla,  M., Klåvus, A., Babu, A. F., Lehtonen, M., … & Hanhineva, K.  (2022). Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition. Scientific Reports, 12(1), 15018. Open-access paper.

Effect of exercise on non-alcoholic fatty liver disease

Babu, A. F., Csader, S., Männistö, V., Tauriainen, M. M., Pentikäinen, H., Savonen, K., … & Schwab, U. (2022). Effects of exercise on NAFLD using non-targeted metabolomics in adipose tissue, plasma, urine, and stool. Scientific reports, 12(1), 1-16. Open-access paper.

Microbiota-associated metabolites in murine tissues

Pessa-Morikawa, T., Husso, A., Kärkkäinen, O., Koistinen, V., Hanhineva, K., Iivanainen, A., & Niku, M. (2022). Maternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta. BMC microbiology, 22(1), 1-16. Open-access paper.

Method paper on the notame R script and our metabolomics workflow

Klåvus, A., Kokla, M., Noerman, S., Koistinen, V. M., Tuomainen, M., Zarei, I., … & Hanhineva, K. (2020). “Notame”: Workflow for non-targeted LC–MS metabolic profiling. Metabolites, 10(4), 135. Open-access paper.

Impact of malting on the phytochemical content of whole grains highlights the value of side-streams

Koistinen, V. M., Tuomainen, M., Lehtinen, P., Peltola, P., Auriola, S., Jonsson, K., & Hanhineva, K. (2020). Side-stream products of malting: a neglected source of phytochemicals. NPJ science of food, 4(1), 1-9. Open-access paper.

Comparison of imputation methods to tackle missing values in LC-MS data

Kokla, M., Virtanen, J., Kolehmainen, M., Paananen, J., & Hanhineva, K. (2019). Random forest-based imputation outperforms other methods for imputing LC-MS metabolomics data: a comparative study. BMC bioinformatics, 20(1), 1-11. Open-access paper.

Older classics

Wide review on nutrimetabolomics

Ulaszewska, M. M., Weinert, C. H., Trimigno, A., Portmann, R., Andres Lacueva, C., Badertscher, R., … Hanhineva, K., … & Vergères, G. (2019). Nutrimetabolomics: an integrative action for metabolomic analyses in human nutritional studies. Molecular nutrition & food research, 63(1), 1800384.

Position paper on phenolic acid metabolism

Bento-Silva, A., Koistinen, V. M., Mena, P., Bronze, M. R., Hanhineva, K., Sahlstrøm, S., … & Aura, A. M. (2020). Factors affecting intake, metabolism and health benefits of phenolic acids: do we understand individual variability?. European journal of nutrition, 59(4), 1275-1293.

Potential type 2 diabetes biomarkers

De Mello, V. D., Paananen, J., Lindström, J., Lankinen, M. A., Shi, L., Kuusisto, J., … & Uusitupa, M. (2017). Indolepropionic acid and novel lipid metabolites are associated with a lower risk of type 2 diabetes in the Finnish Diabetes Prevention Study. Scientific reports, 7(1), 1-12. Open-access paper.

Whole grain phytochemicals and their analysis with mass spectrometry

Koistinen, V. M., & Hanhineva, K. (2017). Mass spectrometry-based analysis of whole-grain phytochemicals. Critical reviews in food science and nutrition, 57(8), 1688-1709.

Biomarkers of foods within the Nordic diet

Hanhineva, K., Lankinen, M. A., Pedret, A., Schwab, U., Kolehmainen, M., Paananen, J., … & Mykkänen, H. (2015). Nontargeted metabolite profiling discriminates diet-specific biomarkers for consumption of whole grains, fatty fish, and bilberries in a randomized controlled trial. The Journal of nutrition, 145(1), 7-17. Open-access paper.

Dietary polyphenols and carbohydrate metabolism

Hanhineva, K., Törrönen, R., Bondia-Pons, I., Pekkinen, J., Kolehmainen, M., Mykkänen, H., & Poutanen, K. (2010). Impact of dietary polyphenols on carbohydrate metabolism. International journal of molecular sciences, 11(4), 1365-1402. Open-access paper.