Evidence map›Paper›PMID 39316685›Full record

ArticleThe Journal of infectious diseases2025

Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection.

Shanlin Ke, Javier A Villafuerte Gálvez, Zheng Sun, Yangchun Cao, Nira R Pollock, Xinhua Chen, Ciarán P Kelly, Yang-Yu Liu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of infectious diseases, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Shanlin KeChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School.
Javier A Villafuerte GálvezDivision of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
Zheng SunChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School.
Yangchun CaoDivision of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
Nira R PollockDivision of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School.
Xinhua ChenDivision of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
Ciarán P KellyDivision of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
Yang-Yu LiuChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School.ORCID 0000-0003-2728-4907

Funding

Functional Redundancy of Human Microbiome and its Implication in Fecal Microbiota TransplantationR01AI141529 · NIAID · BRIGHAM AND WOMEN'S HOSPITAL · PI LIU, YANG-YU · 2019 to 2023
$4.5M
Ultrasensitive C.difficile toxin measurement for diagnosis and outcome predictionR01AI116596 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI POLLOCK, NIRA · 2016 to 2020
$4.1M
Redefining C.difficile patient outcomes through network medicineK23AI177749 · NIAID · BETH ISRAEL DEACONESS MEDICAL CENTER · PI Javier Andres Villafuerte Galvez · 2023 to 2026
$766k
China Scholarship Council 201806305024Institut MérieuxIrving W. and Charlotte F. Rabb AwardMilky Way Life SciencesNational Institute of Allergy and Infectious Diseases K23AI177749-01National Institute of Allergy and Infectious Diseases R01AI116596National Institute of Allergy and Infectious Diseases R01AI141529National Key Research and Development Program 2021YFD1300301NIAID NIH HHS K23 AI177749NIAID NIH HHS R01 AI116596NIAID NIH HHS R01 AI141529Ningxia Key Project of Research and Development Plan 2023BFC01036Shaanxi Science Fund for Distinguished Young Scholars 2024-JC-JCQN-25
6 · The paper itself

Abstract

Clostridioides difficile infection (CDI) is a major cause of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) shows promise for recurrent CDI, its mechanisms and long-term safety are not fully understood. Live biotherapeutic products (LBPs) using predefined bacterial consortia offer an alternative option, but the rational design of LBPs remains challenging. Here, we employ a computational pipeline and three metagenomic datasets to identify microbial strains for LBPs targeting CDI. We constructed the CDI-related microbial genome catalog, comprising 3741 nonredundant metagenome-assembled genomes (nrMAGs), and identified multiple potential protective nrMAGs, including strains from Dorea formicigenerans, Oscillibacter welbionis, and Faecalibacterium prausnitzii. Importantly, some of these protective nrMAGs were found to play an important role in FMT success, and most top protective nrMAGs can be validated by various previous findings. Our results demonstrate a framework for selecting microbial strains targeting CDI, paving the way for the computational design of LBPs against other enteric infections.

Indexed as

Biological ProductsBiological TherapyClostridioides difficileClostridium InfectionsFecal Microbiota TransplantationHumansBiological ProductsClostridioides difficile infectiongut microbiomelive biotherapeutic products

Identifiers

PMID39316685
PMCPMC12247820

What Socratic 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 Socratic graph.