Evidence map›Paper›PMID 40335509›Full record

ArticleNature communications2025

Dietary amino acids regulate Salmonella colonization via microbiota-dependent mechanisms in the mouse gut.

Joseph M Pickard, Steffen Porwollik, Gustavo Caballero-Flores, Roberta Caruso, Shinji Fukuda, Tomoyoshi Soga, Naohiro Inohara, Michael McClelland, Gabriel Núñez

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the 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.

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

13 citing papers in PubMed.

  1. Article
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  8. Catabolism of serine enantiomers represses enterohemorrhagicProceedings of the National Academy of Sciences of the United States of America · 2026
    Article
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  11. Article
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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

9 authors.

Joseph M PickardDepartment of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0002-9501-0441
Steffen PorwollikDepartment of Microbiology and Molecular Genetics, University of California, Irvine, School of Medicine, Irvine, CA, USA.
Gustavo Caballero-FloresDepartment of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0002-0640-1521
Roberta CarusoDepartment of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0002-9891-0082
Shinji FukudaInstitute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.ORCID http://orcid.org/0000-0001-5161-9880
Tomoyoshi SogaInstitute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.ORCID http://orcid.org/0000-0001-9502-2509
Naohiro InoharaDepartment of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
Michael McClellandDepartment of Microbiology and Molecular Genetics, University of California, Irvine, School of Medicine, Irvine, CA, USA.ORCID http://orcid.org/0000-0003-1788-9347
Gabriel NúñezDepartment of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA. gabriel.nunez@umich.edu.ORCID http://orcid.org/0000-0002-6529-2695

Funding

Univ.of Calif., Irvine Cancer Center Support GrantP30CA062203 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Melanie Funes · 1994 to 2026
$57.9M
Molecular determinants of oxidative stress in Salmonella pathogenesisR01AI136520 · NIAID · UNIVERSITY OF COLORADO DENVER · PI Andres Vazquez-Torres · 2018 to 2026
$3.7M
Role of Immunity and the Microbiota in Enteropathogenic E. coli EradicationR01DK095782 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI NUNEZ, GABRIEL · 2013 to 2022
$3.6M
The Role of Inflammasomes in Mucosal Immunity to Intestinal Bacterial PathogensR01DK091191 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI NUNEZ, GABRIEL · 2010 to 2019
$3.1M
Deciphering the pathogenesis of an enteric pathogen in neonatal and immunodeficient miceR00AI159620 · NIAID · UNIVERSITY OF WISCONSIN-MADISON · PI CABALLERO FLORES, GUSTAVO · 2024 to 2025
$498k
Deciphering the pathogenesis of an enteric pathogen in neonatal and immunodeficient miceK99AI159620 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CABALLERO FLORES, GUSTAVO · 2022 to 2023
$185k
Barcoding a Salmonella gene knockout libraryR03AI139557 · NIAID · UNIVERSITY OF CALIFORNIA-IRVINE · PI MCCLELLAND, MICHAEL · 2019 to 2020
$157k
Identifying molecular mechanisms of colonization resistance to enteric pathogensF32DK118800 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI PICKARD, JOSEPH · 2018 to 2019
$127k
NCI NIH HHS P30 CA062203NIAID NIH HHS K99 AI159620NIAID NIH HHS R00 AI159620NIAID NIH HHS R01 AI136520NIAID NIH HHS R03 AI139557NIDDK NIH HHS F32 DK118800NIDDK NIH HHS R01 DK091191NIDDK NIH HHS R01 DK095782
6 · The paper itself

Abstract

The gut microbiota confers host protection against pathogen colonization early after infection. Several mechanisms underlying the protection have been described, but the contributions of nutrient competition versus direct inhibition are controversial. Using an ex vivo model of Salmonella growth in the mouse cecum with its indigenous microbes, we find that nutrient limitation and typical inhibitory factors alone cannot prevent pathogen growth. However, the addition of certain amino acids markedly reverses the microbiota's ability to suppress pathogen growth. Enhanced Salmonella colonization after antibiotic treatment is ablated by exclusion of dietary protein, which requires the presence of the microbiota. Thus, dietary protein and amino acids are important regulators of colonization resistance.

Indexed as

Amino AcidsDietary ProteinsGastrointestinal MicrobiomeSalmonellaSalmonella typhimuriumAnimalsAnti-Bacterial AgentsCecumFemaleMiceMice, Inbred C57BLSalmonella InfectionsAmino AcidsAnti-Bacterial AgentsDietary Proteins

Identifiers

PMID40335509
PMCPMC12058977

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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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.