Evidence map›Paper›PMID 40339579›Full record

ArticleCell systems2025

Decoding the role of the arginine dihydrolase pathway in shaping human gut community assembly and health-relevant metabolites.

Yiyi Liu, Yu-Yu Cheng, Jaron Thompson, Zhichao Zhou, Eugenio I Vivas, Matthew F Warren, Julie M DuClos, Karthik Anantharaman, Federico E Rey, Ophelia S Venturelli

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Review
  2. Article
  3. Research square · 2026
    Article
  4. bioRxiv : the preprint server for biology · 2026
    Article
  5. Human microbiota-associated animal models: a review.Frontiers in cellular and infection microbiology · 2025
    Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Yiyi LiuDepartment of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Yu-Yu ChengDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Jaron ThompsonDepartment of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Zhichao ZhouDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Eugenio I VivasDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI 53706, USA.
Matthew F WarrenDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Julie M DuClosDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Karthik AnantharamanDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Federico E ReyDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Ophelia S VenturelliDepartment of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA. Electronic address: ophelia.venturelli@duke.edu.

Funding

TRAINING IN NUTRITIONT32DK007665 · NIDDK · UNIVERSITY OF WISCONSIN-MADISON · PI GUY E GROBLEWSKI, Chi- Liang Eric Yen · 1993 to 2026
$9.2M
Biotechnology Training ProgramT32GM135066 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI SCOTT M. COYLE, BRIAN G FOX · 2020 to 2026
$7.0M
Elucidating the molecular and ecological design principles of stability and assembly of the human gut microbiotaR35GM124774 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Ophelia Venturelli · 2017 to 2026
$2.9M
Model-guided design of next-generation bacterial therapeutics to treat cardiovascular diseaseR01EB030340 · NIBIB · UNIVERSITY OF WISCONSIN-MADISON · PI REY, FEDERICO E, ROMERO, PHILIP ANTHONY · 2020 to 2023
$2.8M
NIBIB NIH HHS R01 EB030340NIDDK NIH HHS T32 DK007665NIGMS NIH HHS R35 GM124774NIGMS NIH HHS T32 GM135066
6 · The paper itself

Abstract

The arginine dihydrolase pathway (arc operon) provides a metabolic niche by transforming arginine into metabolic byproducts. We investigate the role of the arc operon in probiotic Escherichia coli Nissle 1917 on human gut community assembly and health-relevant metabolite profiles. By stabilizing environmental pH, the arc operon reduces variability in community composition in response to pH perturbations and frequently enhances butyrate production in synthetic communities. We use a tailored machine learning model for microbiomes to predict community assembly in response to variation in initial media pH and arc operon activity. This model uncovers the pH- and arc operon-dependent interactions shaping community assembly. Human gut species display altered colonization dynamics in response to the arc operon in the murine gut. In sum, our framework to quantify the contribution of a specific pathway to microbial community assembly and metabolite production can reveal new engineering strategies. A record of this paper's transparent peer review process is included in the supplemental information.

Indexed as

Gastrointestinal MicrobiomeAnimalsArginineEscherichia coliEscherichia coli ProteinsHumansHydrogen-Ion ConcentrationMachine LearningMetabolic Networks and PathwaysMiceOperonArginineEscherichia coli Proteinsbutyrate productiondynamic computational modelmicrobial interactionspH responsesynthetic biologysynthetic human gut communitiessystems biology

Identifiers

PMID40339579
PMCPMC12716064

What OpenQuestion holds

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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.