Evidence map›Paper›PMID 39500329›Full record

ArticleCell reports2024

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.

Margaret Alexander, Vaibhav Upadhyay, Rachel Rock, Lorenzo Ramirez, Kai Trepka, Patrycja Puchalska, Diego Orellana, Qi Yan Ang, Caroline Whitty, Jessie A Turnbaugh and 7 more

Abstract read
In one paragraph

Article in Cell reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.

0numbers the graph read from it
0cells of the map it votes in
28citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

28 citing papers in PubMed.

  1. Trial
  2. Trial
  3. Trial
  4. Article
  5. Article
  6. The Gut Microbiome in Multiple Sclerosis.Neurology(R) neuroimmunology & neuroinflammation · 2026
    Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Female-enrichedbioRxiv : the preprint server for biology · 2026
    Article
  14. Review
  15. Review
  16. Article
  17. Article
  18. The Interplay between the Gut and Ketogenic Diets in Health and Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Review
  19. Article
  20. High Fat Low Carbohydrate Diet Is Linked to CNS Autoimmunity Protection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors.

Margaret AlexanderDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medical Microbiology and Immunology, University of Wisconsin - Madison, Madison, WI 53706, USA.
Vaibhav UpadhyayDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
Rachel RockDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Lorenzo RamirezDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Kai TrepkaDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Patrycja PuchalskaDivision of Molecular Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
Diego OrellanaDepartment of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
Qi Yan AngDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Caroline WhittyDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Jessie A TurnbaughDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Yuan TianDepartment of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA.
Darren DumlaoDepartment of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
Renuka NayakDepartment of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; San Francisco VA Medical Center, San Francisco, CA 94121, USA.
Andrew PattersonDepartment of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA.
John C NewmanBuck Institute for Research on Aging, Novato, CA 94945, USA; Division of Geriatrics, University of California, San Francisco, San Francisco, CA 94158, USA.
Peter A CrawfordDivision of Molecular Medicine, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Peter J TurnbaughDepartment of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA. Electronic address: peter.turnbaugh@ucsf.edu.

Funding

Research BaseP30DK063720 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GERMAN, MICHAEL S · 2003 to 2019
$21.8M
VARC CoreP30AG044281 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Louise C. Walter · 2013 to 2026
$19.9M
Medical Scientist Training Program (T32 NRSA Training Grant)T32GM141323 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Aimee Kao · 2021 to 2026
$10.5M
Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
KETONE BODY METABOLISM AND INTEGRATED METABOLIC HOMEOSTASISR01DK091538 · NIDDK · WASHINGTON UNIVERSITY · PI CRAWFORD, PETER A · 2011 to 2024
$6.2M
Predicting and preventing drug metabolism by the human gut microbiomeR01HL122593 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Peter James Turnbaugh · 2016 to 2026
$5.7M
Mechanisms of the signaling metabolite β-hydroxybutyrate in Alzheimer's disease and the aging brainR01AG067333 · NIA · BUCK INSTITUTE FOR RESEARCH ON AGING · PI John C Newman · 2020 to 2026
$4.8M
Restorative practice in repairing harm and promoting safe and inclusive practices in the laboratory.T32GM136547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Adrian Erlebacher, Anita Sil · 2020 to 2026
$4.5M
Employing the gut microbiome to accelerate effective initiation of rheumatoid arthritis therapyR01AR074500 · NIAMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Renuka Rajendra Nayak, Jose U. Scher · 2019 to 2026
$4.1M
Host-microbiome interactions shape the metabolic effects of ketogenic dietsR01DK114034 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TURNBAUGH, PETER JAMES · 2020 to 2024
$2.5M
Ketogenic Oscillations and Neurometabolic HealthspanR01AG069781 · NIA · UNIVERSITY OF MINNESOTA · PI CRAWFORD, PETER A, THYFAULT, JOHN P · 2020 to 2024
$2.3M
Establishing the feasibility of editing the human gut microbiomeR01AT011117 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI TURNBAUGH, PETER JAMES · 2020 to 2023
$1.6M
CSRD VA I01 CX002557NCCIH NIH HHS R01 AT011117NHLBI NIH HHS K08 HL165106NHLBI NIH HHS R01 HL122593NIAID NIH HHS F32 AI147456NIAID NIH HHS K99 AI159227NIAID NIH HHS R00 AI159227NIAID NIH HHS T32 AI060537NIAMS NIH HHS K08 AR073930NIAMS NIH HHS R01 AR074500NIA NIH HHS P30 AG044281NIA NIH HHS R01 AG067333NIA NIH HHS R01 AG069781NIDDK NIH HHS P30 DK063720NIDDK NIH HHS R01 DK091538NIDDK NIH HHS R01 DK114034NIGMS NIH HHS R35 GM151349NIGMS NIH HHS T32 GM136547NIGMS NIH HHS T32 GM141323
6 · The paper itself

Abstract

Diet can protect from autoimmune disease; however, whether diet acts via the host and/or microbiome remains unclear. Here, we use a ketogenic diet (KD) as a model to dissect these complex interactions. A KD rescued the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis in a microbiota-dependent fashion. Dietary supplementation with a single KD-dependent host metabolite (β-hydroxybutyrate [βHB]) rescued EAE, whereas transgenic mice unable to produce βHB in the intestine developed more severe disease. Transplantation of the βHB-shaped gut microbiota was protective. Lactobacillus sequence variants were associated with decreased T helper 17 cell activation in vitro. Finally, we isolated an L. murinus strain that protected from EAE, which was phenocopied by a Lactobacillus metabolite enriched by βHB supplementation, indole lactate. Thus, diet alters the immunomodulatory potential of the gut microbiota by shifting host metabolism, emphasizing the utility of taking a more integrative approach to study diet-host-microbiome interactions.

Indexed as

AutoimmunityDiet, KetogenicEncephalomyelitis, Autoimmune, ExperimentalGastrointestinal Microbiome3-Hydroxybutyric AcidAnimalsFemaleLactobacillusMiceMice, Inbred C57BLMice, TransgenicTh17 Cells3-Hydroxybutyric Acidautoimmune diseaseCP: ImmunologyCP: Microbiologygut microbiomeimmune activationketogenesisketogenic dietlactobacillusmultiple sclerosisneuroinflammationnutritiontrytophan metabolism

Identifiers

PMID39500329
PMCPMC11660937

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.