Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults

Leila M Shinn, Aditya Mansharamani, David J Baer, Janet A Novotny, Craig S Charron, Naiman A Khan, Ruoqing Zhu, Hannah D Holscher

Research output: Contribution to journalArticlepeer-review



The fecal metabolome is affected by diet and includes metabolites generated by human and microbial metabolism. Advances in -omics technologies and analytic approaches have allowed researchers to identify metabolites and better utilize large data sets to generate usable information. One promising aspect of these advancements is the ability to determine objective biomarkers of food intake.


We aimed to utilize a multivariate, machine learning approach to identify metabolite biomarkers that accurately predict food intake.


Data were aggregated from 5 controlled feeding studies in adults that tested the impact of specific foods (almonds, avocados, broccoli, walnuts, barley, and oats) on the gastrointestinal microbiota. Fecal samples underwent GC-MS metabolomic analysis; 344 metabolites were detected in preintervention samples, whereas 307 metabolites were detected postintervention. After removing metabolites that were only detected in either pre- or postintervention and those undetectable in ≥80% of samples in all study groups, changes in 96 metabolites relative concentrations (treatment postintervention minus preintervention) were utilized in random forest models to 1) examine the relation between food consumption and fecal metabolome changes and 2) rank the fecal metabolites by their predictive power (i.e., feature importance score).


Using the change in relative concentration of 96 fecal metabolites, 6 single-food random forest models for almond, avocado, broccoli, walnuts, whole-grain barley, and whole-grain oats revealed prediction accuracies between 47% and 89%. When comparing foods with one another, almond intake was differentiated from walnut intake with 91% classification accuracy.


Our findings reveal promise in utilizing fecal metabolites as objective complements to certain self-reported food intake estimates. Future research on other foods at different doses and dietary patterns is needed to identify biomarkers that can be applied in feeding study compliance and clinical settings.
Original languageEnglish (US)
Article numbernxac195
Pages (from-to)2956-2965
Number of pages10
JournalThe Journal of nutrition
Issue number12
Early online dateAug 30 2022
StatePublished - Jan 14 2023


  • gastrointestinal microbiota
  • machine learning
  • dietary intake biomarker
  • fidelity measures
  • metabolomics

ASJC Scopus subject areas

  • Nutrition and Dietetics
  • Medicine (miscellaneous)


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