Evidence map›Paper›PMID 40777923›Full record

ArticleCell host & microbe2025

Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects.

Stephany Flores Ramos, Nicole Siguenza, Wuling Zhong, Ipsita Mohanty, Amulya Lingaraju, R Alexander Richter, Smruthi Karthikeyan, April L Lukowski, Qiyun Zhu, Wilhan D G Nunes and 7 more

Abstract read
In one paragraph

Article in Cell host & microbe, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing 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

14 citing papers in PubMed.

  1. Ultrafiltered Mulberry (Foods (Basel, Switzerland) · 2026
    Article
  2. Review
  3. Review
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Review
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
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

17 authors.

Stephany Flores RamosDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
Nicole SiguenzaDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
Wuling ZhongDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
Ipsita MohantySkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Amulya LingarajuDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
R Alexander RichterDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
Smruthi KarthikeyanDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
April L LukowskiSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Qiyun ZhuSchool of Life Sciences, Arizona State University, Tempe, AZ, USA.
Wilhan D G NunesSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Jasmine ZemlinSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.
Zhenjiang Zech XuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Jeff HastyShu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
Pieter C DorresteinDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Satchidananda PandaThe Salk Institute for Biological Studies, La Jolla, CA, USA.
Rob KnightBiomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.
Amir ZarrinparDivision of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.

Funding

UC San Diego Clinical and Translational Research InstituteUL1TR001442 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S, HOGARTH, MICHAEL · 2015 to 2024
$88.3M
Viral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Alan Saghatelian · 1985 to 2026
$82.8M
The Southernearch Center for ALPD and CirrhosisP50AA011999 · NIAAA · UNIVERSITY OF SOUTHERN CALIFORNIA · PI HIDEKAZU TSUKAMOTO · 1999 to 2026
$45.8M
Transgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MILES Frome WILKINSON · 2003 to 2026
$40.4M
San Diego Digestive Diseases Research CenterP30DK120515 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Bernd G. Schnabl · 2019 to 2026
$10.8M
Mapping host-microbe-metabolite interactions in 3D to find diet-derived enhancers of immunityDP1AT010885 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KNIGHT, ROB · 2019 to 2023
$5.5M
The Role of Altered Luminal Dynamics in OSA-Induced AtherosclerosisR01HL148801 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZARRINPAR, AMIR · 2019 to 2023
$4.0M
Impact of Time-Restricted Feeding in Reducing Cancer Risk Through Optimizing Mitochondria FunctionR01CA258221 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI PANDA, SATCHIDANANDA · 2021 to 2025
$3.8M
Advanced Development of Informatics Technologies for Cancer Research and Management (U24 Clinical Trial Optional)U24CA248454 · NCI · NORTHERN ARIZONA UNIVERSITY · PI CAPORASO, JAMES GREGORY · 2020 to 2024
$3.7M
Engineering Native E. coli to Detect, Report, and Treat Colorectal CancerU01CA265719 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZARRINPAR, AMIR · 2021 to 2025
$3.1M
Development of Engineered Native Bacteria as a Tool for Functional Manipulation of the Gut MicrobiomeR01AI163483 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEFF M HASTY, Amir Zarrinpar · 2023 to 2026
$3.1M
Reverse Metabolomics for the Discovery of Disease Associated Microbial MoleculesR01DK136117 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2023 to 2026
$2.9M
BLRD VA I01 BX005707NCATS NIH HHS UL1 TR001442NCCIH NIH HHS DP1 AT010885NCI NIH HHS P30 CA014195NCI NIH HHS R01 CA236352NCI NIH HHS R01 CA258221NCI NIH HHS U01 CA265719NCI NIH HHS U24 CA248454NHLBI NIH HHS R01 HL148801NIAAA NIH HHS P50 AA011999NIAID NIH HHS R01 AI163483NIBIB NIH HHS R01 EB030134NIDDK NIH HHS P30 DK063491NIDDK NIH HHS P30 DK120515NIDDK NIH HHS R01 DK136117
6 · The paper itself

Abstract

Diurnal rhythmicity in the gut maintains gut integrity, circadian rhythms, and metabolic homeostasis. However, existing studies focus on microbial composition rather than transcriptional activity. To understand microbial functional dynamics, we characterize diurnal fluctuations in the mouse cecal metatranscriptome and metagenome under high-fat diet and time-restricted feeding (TRF). We show that metatranscriptomics uncover TRF-induced time-dependent microbial functional shifts that are undetectable with metagenomics alone. We also found bile salt hydrolase (

Indexed as

BacteriaCircadian RhythmGastrointestinal MicrobiomeTranscriptomeTransgenesAnimalsCecumDiet, High-FatEscherichia coliGene Expression ProfilingMaleMetagenomeMetagenomicsMiceMice, Inbred C57BL

Identifiers

PMID40777923
PMCPMC12327816

What OpenQuestion 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 OpenQuestion graph.