Evidence map›Paper›PMID 40252648›Full record

ArticleCell host & microbe2025

Antibiotic-induced gut microbiome perturbation alters the immune responses to the rabies vaccine.

Yupeng Feng, Sanne E de Jong, Ana Paula B N Oliveira, Hady Samaha, Fan Yang, Mengyun Hu, Yanli Wang, Nour Beydoun, Xia Xie, Haibo Zhang and 8 more

Abstract read
PubMed Full text at PMC Publisher
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 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

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  16. Experimental dissection of tuberculosis protective immunity: a human perspective.Frontiers in cellular and infection microbiology · 2025
    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

18 authors.

Yupeng FengInstitute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510440, China; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Sanne E de JongInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Ana Paula B N OliveiraDepartment of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
Hady SamahaHope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA.
Fan YangInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Mengyun HuInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Yanli WangInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Nour BeydounHope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA.
Xia XieInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Haibo ZhangInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Dmitri KazminInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Zhuoqing FangInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Jun ZouCenter for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
Andrew T GewirtzCenter for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
Scott D BoydInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Immunology Research, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Thomas HaganDepartment of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
Nadine RouphaelHope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA.
Bali PulendranInstitute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA. Electronic address: bpulend@stanford.edu.

Funding

Using a tonsil organoid system to probe conditions for the induction of protective antibody and T cell responses to influenza.U19AI057229 · NIAID · STANFORD UNIVERSITY · PI Mark Morris Davis · 2003 to 2026
$88.5M
VACCINE INDUCED IMMUNITY IN THE YOUNG AND AGEDU19AI057266 · NIAID · EMORY UNIVERSITY · PI Rafi Ahmed · 2003 to 2026
$81.7M
Systems biological assessment of T cell responses to vaccinationU19AI167903 · NIAID · STANFORD UNIVERSITY · PI BALI PULENDRAN · 2022 to 2026
$13.2M
MICROBES, DENDRITIC CELL SUBSETS AND T-CELL IMMUNITYR01AI048638 · NIAID · STANFORD UNIVERSITY · PI PULENDRAN, BALI · 2001 to 2024
$4.5M
30-parameter FACSymphony A3 flow cytometer for Shared Resource LabS10OD026831 · OD · STANFORD UNIVERSITY · PI NOLAN, GARRY P · 2019 to 2019
$510k
NIAID NIH HHS R01 AI048638NIAID NIH HHS U19 AI057229NIAID NIH HHS U19 AI057266NIAID NIH HHS U19 AI167903NIH HHS S10 OD026831
6 · The paper itself

Abstract

The gut microbiome plays a crucial role in modulating human immunity. Previously, we reported that antibiotic-induced microbiome perturbation affects influenza vaccine responses, depending on pre-existing immunity levels. Here, we employed a systems biology approach to analyze the impact of antibiotic administration on both primary and secondary immune responses to the rabies vaccine in humans. Antibiotic administration reduced the gut bacterial load, with a long-lasting reduction in commensal diversity. This alteration was associated with reduced rabies-specific humoral responses. Multi-omics profiling revealed that antibiotic administration induced (1) an enhanced pro-inflammatory signature early after vaccination, (2) a shift in the balance of vaccine-specific T-helper 1 (Th1) to T-follicular-helper response toward Th1 phenotype, and (3) profound alterations in metabolites, particularly in secondary bile acids in the blood. By integrating multi-omics datasets, we generated a multiscale, multi-response network that revealed key regulatory nodes, including the microbiota, secondary bile acids, and humoral immunity to vaccination.

Indexed as

Anti-Bacterial AgentsGastrointestinal MicrobiomeRabies VaccinesAntibodies, ViralBile Acids and SaltsFemaleHumansImmunity, HumoralMaleRabiesTh1 CellsVaccinationAnti-Bacterial AgentsAntibodies, ViralBile Acids and SaltsRabies Vaccinesantibodyinnate immunitymetabolismmicrobiomerabies vaccinesystems biologysystems immunologysystems vaccinologyT cells

Identifiers

PMID40252648
PMCPMC12084132

What Socratic holds

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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.