Evidence map›Paper›PMID 40238917›Full record

Observational studyScience translational medicine2025

Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.

Kai R Trepka, Wesley A Kidder, Than S Kyaw, Taylor Halsey, Christine A Olson, Edwin F Ortega, Cecilia Noecker, Vaibhav Upadhyay, Dalila Stanfield, Paige Steiding and 9 more

Registry-linked trialAbstract readObservational Study
In one paragraph

Observational study in Science translational medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04054908 (Gut Microbiome and Oral Fluoropyrimidine Study in Patients With Colorectal Cancer), which is not on this map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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.

NCT04054908 completednot on this map

Gut Microbiome and Oral Fluoropyrimidine Study in Patients With Colorectal Cancer

TypeobservationalSponsorUniversity of California, San FranciscoRan2018 to 2022Enrolled50ConditionsGastrointestinal Microbiome, Neoplasm, Colorectal
3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

  1. Trial
  2. Review
  3. Harnessing the microbiome for cancer therapy.Nature reviews. Microbiology · 2026
    Review
  4. Research square · 2026
    Article
  5. bioRxiv : the preprint server for biology · 2026
    Article
  6. Article
  7. Review
  8. Review
  9. Review
  10. Article
  11. Article
  12. Article
  13. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors.

Kai R TrepkaDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0002-8672-6317
Wesley A KidderDepartment of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0001-8851-7853
Than S KyawDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0002-7933-8615
Taylor HalseyDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0001-8601-9949
Christine A OlsonDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0002-5382-1393
Edwin F OrtegaDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0002-3890-0413
Cecilia NoeckerDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0003-1417-2383
Vaibhav UpadhyayDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0002-7652-1043
Dalila StanfieldUCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA.
Paige SteidingUCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA.ORCID 0000-0002-5938-9896
Benjamin G H GuthrieDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0001-9694-7263
Peter SpanogiannopoulosDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
Darren DumlaoDepartment of Gastroenterology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0009-0000-0182-072X
Jessie A TurnbaughDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0003-3933-1985
Matthew D StachlerDepartment of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0003-0958-0286
Erin L Van BlariganUCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA.ORCID 0000-0001-5079-3385
Alan P VenookDepartment of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0001-9749-6548
Chloe E AtreyaDepartment of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0003-2954-1727
Peter J TurnbaughDepartment of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID 0000-0002-0888-2875

Funding

Microbial Pathogenesis and Host DefenseT32AI060537 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Joanne N. Engel · 2004 to 2026
$6.5M
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
Metabolism of cancer chemotherapeutics by the human gut microbiomeR01CA255116 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Peter James Turnbaugh · 2023 to 2026
$3.1M
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
Impact of gut bacterial metabolites on lung function and diseaseK08HL165106 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Vaibhav Upadhyay · 2023 to 2026
$676k
Impact of the microbiome on chemotherapeutic outcomesF30CA257378 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KYAW, THAN SOE · 2021 to 2024
$190k
NCI NIH HHS F30 CA257378NCI NIH HHS R01 CA255116NHLBI NIH HHS K08 HL165106NHLBI NIH HHS R01 HL122593NIAID NIH HHS T32 AI060537NIDDK NIH HHS R01 DK114034
6 · The paper itself

Abstract

Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16

Indexed as

BacteriaColorectal NeoplasmsFluorouracilOperonPyrimidinesAnimalsFemaleGastrointestinal MicrobiomeHumansMaleMiceRNA, Ribosomal, 16SFluorouracilPyrimidinesRNA, Ribosomal, 16S

Identifiers

PMID40238917
PMCPMC12087798

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Registered trials

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.