Food, gut & nutritional metabolomics

Spotlight

Comment: We need more consistent metabolite nomenclature

As the saying goes in Finnish and Swedish, a beloved child has many names. However, in metabolomics, the multitude of trivial names in use for metabolites has resulted in a disconnect between publications and challenges in performing literature searches on individual metabolites. In this comment published in March 2023 in Nature Metabolism, we propose recommendations to mitigate these issues as the metabolomics-related publications are rapidly growing in number. The publication PDF is available on request from the corresponding author.

Research papers

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 phytochemicals of whole grains

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.

Random forest imputation of 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.

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.

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.

Review papers

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 and Metabolism, in press.

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.

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.

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.