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Machine Learning Metabolomics Profiling of Dietary Interventions from a Six-Week Randomised Trial

Kouraki, Afroditi; Nogal, Ana; Nocun, Weronika; Louca, Panayiotis; Vijay, Amrita; Wong, Kari; Michelotti, Gregory A.; Menni, Cristina; Valdes, Ana M.

Machine Learning Metabolomics Profiling of Dietary Interventions from a Six-Week Randomised Trial Thumbnail


Ana Nogal

Weronika Nocun

Panayiotis Louca

Kari Wong

Gregory A. Michelotti

Cristina Menni


Metabolomics can uncover physiological responses to prebiotic fibre and omega-3 fatty acid supplements with known health benefits and identify response-specific metabolites. We profiled 534 stool and 799 serum metabolites in 64 healthy adults following a 6-week randomised trial comparing daily omega-3 versus inulin supplementation. Elastic net regressions were used to separately identify the serum and stool metabolites whose change in concentration discriminated between the two types of supplementations. Random forest was used to explore the gut microbiome’s contribution to the levels of the identified metabolites from matching stool samples. Changes in serum 3-carboxy-4-methyl-5-propyl-2-furanpropanoate and indoleproprionate levels accurately discriminated between fibre and omega-3 (area under the curve (AUC) = 0.87 [95% confidence interval (CI): 0.63–0.99]), while stool eicosapentaenoate indicated omega-3 supplementation (AUC = 0.86 [95% CI: 0.64–0.98]). Univariate analysis also showed significant increases in indoleproprionate with fibre, 3-carboxy-4-methyl-5-propyl-2-furanpropanoate, and eicosapentaenoate with omega-3. Out of these, only the change in indoleproprionate was partly explained by changes in the gut microbiome composition (AUC = 0.61 [95% CI: 0.58–0.64] and Rho = 0.21 [95% CI: 0.08–0.34]) and positively correlated with the increase in the abundance of the genus Coprococcus (p = 0.005). Changes in three metabolites discriminated between fibre and omega-3 supplementation. The increase in indoleproprionate with fibre was partly explained by shifts in the gut microbiome, particularly Coprococcus, previously linked to better health.

Journal Article Type Article
Acceptance Date May 27, 2024
Online Publication Date May 29, 2024
Publication Date May 29, 2024
Deposit Date May 31, 2024
Publicly Available Date Jun 3, 2024
Journal Metabolites
Electronic ISSN 2218-1989
Publisher MDPI
Peer Reviewed Peer Reviewed
Volume 14
Issue 6
Article Number 311
Keywords fibre; omega-3; metabolomics; machine learning; indoleproprionate; gut microbiome
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