Evidence map›Paper›PMID 40056901›Full record

ArticleCell2025

Functional diversification of dietary plant small molecules by the gut microbiome.

Gavin A Kuziel, Gabriel L Lozano, Corina Simian, Long Li, John Manion, Emmanuel Stephen-Victor, Talal Chatila, Min Dong, Jing-Ke Weng, Seth Rakoff-Nahoum

Abstract read
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing 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

25 citing papers in PubMed.

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  13. Pushing the frontier of gut microbiome health cross-kingdom and cross-organ.Nature reviews. Gastroenterology & hepatology · 2026
    Article
  14. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Gavin A KuzielDivision of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
Gabriel L LozanoDivision of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
Corina SimianWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology & Department of Bioengineering, Northeastern University, Boston, MA 02120, USA; Institute for Plant-Human Interface, Northeastern University, Boston, MA 02120, USA.
Long LiDivision of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
John ManionDepartment of Urology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
Emmanuel Stephen-VictorDivision of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
Talal ChatilaDivision of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
Min DongDepartment of Urology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
Jing-Ke WengWhitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology & Department of Bioengineering, Northeastern University, Boston, MA 02120, USA; Institute for Plant-Human Interface, Northeastern University, Boston, MA 02120, USA.
Seth Rakoff-NahoumDivision of Infectious Diseases, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02139, USA. Electronic address: seth.rakoff-nahoum@childrens.harvard.edu.

Funding

STRUCTURE-FUNCTION RELATIONSHIPS IN THE ALIMENTARY TRACTP30DK034854 · NIDDK · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI JONATHAN C KAGAN · 1986 to 2026
$32.4M
Structure and Function of C. Difficile ToxinsR01AI139087 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI Min Dong, Rongsheng Jin · 2018 to 2026
$7.4M
Immunological and Microbial Mechanisms in Food AllergyR01AI126915 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI Talal Amine Chatila, Seth Rakoff-Nahoum · 2017 to 2026
$4.9M
Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiomeR01AI171100 · NIAID · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI KHALIL, AHMAD SAMIR, RAKOFF-NAHOUM, SETH · 2022 to 2025
$4.1M
Molecular basis of action and pathogenesis of Clostridium difficile toxin BR01AI132387 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI DONG, MIN · 2017 to 2021
$3.5M
Targeting microbial dysbiosis in Food Allergy to restore toleranceR01AI158814 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI CHATILA, TALAL AMINE, RAKOFF-NAHOUM, SETH · 2021 to 2025
$3.0M
Positive Selection as a Host Mechanism to Control the MicrobiomeDP2GM136652 · NIGMS · BOSTON CHILDREN'S HOSPITAL · PI RAKOFF-NAHOUM, SETH · 2019 to 2019
$2.7M
Carbohydrate Public Good Interactions in Healthy and Dysbiotic Bacteroidales CommunitiesK08AI130392 · NIAID · BOSTON CHILDREN'S HOSPITAL · PI RAKOFF-NAHOUM, SETH · 2017 to 2021
$905k
NIAID NIH HHS K08 AI130392NIAID NIH HHS R01 AI126915NIAID NIH HHS R01 AI132387NIAID NIH HHS R01 AI139087NIAID NIH HHS R01 AI158814NIAID NIH HHS R01 AI171100NIDDK NIH HHS P30 DK034854NIGMS NIH HHS DP2 GM136652
6 · The paper itself

Abstract

Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the Bacteroides, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This Bacteroides metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen Clostridioides difficile via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone "effector" functions by a distinct gut-microbiome-encoded PSM-processing system.

Indexed as

BacteroidesGastrointestinal MicrobiomeAnimalsGlucosidesGlycosidesHumansPhenolsSecondary MetabolismStilbenesGlucosidesGlycosidesPhenolsStilbenesanti-inflammatoryClostridioides difficilecolitiscolonization resistancedietglycoside hydrolasegut microbiomephenolic glycosidesphytochemicalsplant secondary metabolites

Identifiers

PMID40056901
PMCPMC12671244

What Socratic holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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 Socratic graph.