Data availability
The full trial protocol, demographic characteristics of participants, and cardiometabolic outcomes from the (FS)2 trial are publicly available through Open Science Framework (https://osf.io/rvbuy/). All data supporting the findings described in this manuscript are available in the article and in the Supplementary Information and Supplementary Data. De-identified metabolomics data are available under controlled access to qualified investigators for non-commercial research purposes. The raw data are protected and not publicly available due to consent restrictions. Access to metabolomics data can be requested by contacting the corresponding authors (joel.hirschhorn@childrens.harvard.edu; cara.ebbeling@childrens.harvard.edu). Req…
Data availability
The full trial protocol, demographic characteristics of participants, and cardiometabolic outcomes from the (FS)2 trial are publicly available through Open Science Framework (https://osf.io/rvbuy/). All data supporting the findings described in this manuscript are available in the article and in the Supplementary Information and Supplementary Data. De-identified metabolomics data are available under controlled access to qualified investigators for non-commercial research purposes. The raw data are protected and not publicly available due to consent restrictions. Access to metabolomics data can be requested by contacting the corresponding authors (joel.hirschhorn@childrens.harvard.edu; cara.ebbeling@childrens.harvard.edu). Requests will be reviewed in accordance with IRB approval and applicable ethical and legal requirements. Eligible investigators will be required to sign a Data Use Agreement (DUA). Upon execution of the DUA, requests will be fulfilled within 4 weeks, and data will remain available for the period specified in the DUA (at least one year). Trials were registered at ClinicalTrials.gov: (FS)2, NCT02068885, registered on 21 February 2014 (https://clinicaltrials.gov/study/NCT02068885); and the Popular Diets Study (validation study), NCT00315354, registered on 18 April 2006 (https://clinicaltrials.gov/study/NCT00315354). Source data are provided in this paper.
Code availability
The code and documentation for PAIRUP-MS, which was previously developed and published and applied in the present paper, are publicly available on GitHub (https://github.com/yuhanhsu/PAIRUP-MS). No new custom or unique computational code was developed for this study. All packages used are publicly available and have been cited in the manuscript.
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Acknowledgements
We thank the study investigators and participants of the (FS)2 for their time and effort. We thank Jakub Morze, the first author of the meta-analysis Metabolomics and Type 2 Diabetes, for generously providing data for analysis in this study. We would like to thank the Consortium of METabolomics Studies (COMETS) for promoting collaborations among the investigators. M.Y.M. was supported by NIH grant HL171855. N.ET. and C.W. were supported by the SciLifeLab & Wallenberg Data-Driven Life Science Program (grant: KAW 2020.0239). Analyses for this paper were supported by the National Institute of Diabetes and Digestive and Kidney Diseases (R01DK125273), and additional support was provided by R01DK075787. Implementation of the Framingham State Food Study was supported by grants from Nutrition Science Initiative (made possible by gifts from Arnold Ventures and Robert Lloyd Corkin Charitable Foundation), New Balance Foundation, Many Voices Foundation, and Blue Cross Blue Shield. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation and writing of the manuscript.
Author information
Authors and Affiliations
Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA
Angeliki M. Angelidi, Eric Bartell, Yisong Huang & Joel N. Hirschhorn 1.
Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Angeliki M. Angelidi, Eric Bartell, Yisong Huang & Joel N. Hirschhorn 1.
Department of Pediatrics, Harvard Medical School, Boston, MA, USA
Angeliki M. Angelidi, David S. Ludwig & Cara B. Ebbeling 1.
Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
Eric Bartell & Joel N. Hirschhorn 1.
Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
Oana A. Zeleznik, Shilpa N. Bhupathiraju, Rachel S. Kelly & Jessica Lasky-Su 1.
Department of Life Sciences, SciLifeLab, Chalmers University of Technology, Gothenburg, Sweden
Núria Estanyol-Torres & Clemens Wittenbecher 1.
Division of Cardiovascular Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
Michael Y. Mi 1.
Metabolomics Platform, Broad Institute, Cambridge, MA, USA
Clary B. Clish 1.
New Balance Foundation Obesity Prevention Center, Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA
David S. Ludwig & Cara B. Ebbeling 1.
Steno Diabetes Center Copenhagen, Herlev, Denmark
David S. Ludwig
Authors
- Angeliki M. Angelidi
- Eric Bartell
- Yisong Huang
- Oana A. Zeleznik
- Núria Estanyol-Torres
- Michael Y. Mi
- Shilpa N. Bhupathiraju
- Rachel S. Kelly
- Clemens Wittenbecher
- Jessica Lasky-Su
- Clary B. Clish
- David S. Ludwig
- Cara B. Ebbeling
- Joel N. Hirschhorn
Contributions
C.B.E. and J.N.H. designed and coordinated the study; D.S.L. and C.B.E. designed and implemented the (FS)2; A.M.A. analyzed data and designed the figures with input from E.B., Y.H., O.A.Z., and J.N.H.; A.M.A. wrote the first draft; A.M.A., C.B.C., C.B.E., and J.N.H. wrote the paper; C.B.C. conducted the metabolomics measurements; J.LS, C.B.E., and J.N.H. supervised the project. All authors (A.M.A., E.B., Y.H., O.A.Z., N.ET., M.Y.M., S.N.B., R.S.K., C.W., J.L.-S., C.B.C., D.S.L., C.B.E., and J.N.H.) contributed to the discussion and interpretation of results, critically reviewed the paper, and agreed to submit the paper for publication.
Corresponding authors
Correspondence to Cara B. Ebbeling or Joel N. Hirschhorn.
Ethics declarations
Competing interests
D.S.L. received royalties for books on obesity and nutrition that recommend a low-glycemic load diet. J.L.-S. is a scientific advisor to TruDiagnostic and Precion Inc. The rest of the authors declare no competing interests.
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Cite this article
Angelidi, A.M., Bartell, E., Huang, Y. et al. Weight-independent effects of dietary carbohydrate-to-fat ratio on metabolomic profiles: secondary outcomes of a 5-month randomized controlled feeding trial. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68353-z
Received: 23 September 2024
Accepted: 05 January 2026
Published: 17 January 2026
DOI: https://doi.org/10.1038/s41467-026-68353-z