Evidence map›Paper›PMID 41760847›Full record

ArticleScientific reports2026

Pangenome-based design of strain-specific primers enables precise monitoring of bacteria in human microbiome intervention trials.

Tom Eilers, Lize Delanghe, Ilke De Boeck, Tim Van Rillaer, Joke Van Malderen, Sam Bakelants, Wannes Van Beeck, Stijn Wittouck, Sarah Lebeer

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2026. 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. Microbiology spectrum · 2025
    Trial
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.

Tom Eilers *Department of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Lize Delanghe *Department of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Ilke De BoeckDepartment of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Tim Van RillaerDepartment of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Joke Van MalderenDepartment of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Sam BakelantsDepartment of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Wannes Van BeeckDepartment of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Stijn WittouckDepartment of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
Sarah LebeerDepartment of Bioscience Engineering, Laboratory of Applied Microbiology and Biotechnology, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium. sarah.lebeer@uantwerpen.be.

Funding

Agentschap Innoveren en Ondernemen HBC.2020.2873Agentschap Innoveren en Ondernemen HBC.2022.1000Fonds Wetenschappelijk Onderzoek 1224923NFonds Wetenschappelijk Onderzoek 12AZ624NFonds Wetenschappelijk Onderzoek 12S4222NFonds Wetenschappelijk Onderzoek 1S08523NHorizon 2020 Framework Programme 852600
6 · The paper itself

Abstract

Lactic acid bacteria (LAB), which include many well-known beneficial bacteria, are widely used in food fermentation, biotechnology, and probiotic formulations. Within this group, strains of Lactobacillaceae are particularly well studied. However, accurate monitoring of the survival and persistence of individual strains across different niches remains challenging due to the limited availability of strain-specific detection tools. This study introduces a robust pangenome-based approach to identify unique genetic targets for the development of strain-specific primers. Using this approach, selective and specific primers were developed for six strains spanning different LAB species. Primers for the widely used probiotic strains Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1 were validated using samples from three placebo-controlled human intervention studies. These assays enabled precise tracking of each strain across body sites, including the skin and the upper respiratory tract, revealing clear distinctions between treatment and control samples. This gene-targeted qPCR method provides a sensitive and reliable method for strain-level detection and can be readily adapted to other bacterial strains for diverse research and industrial applications.

Indexed as

DNA PrimersLactobacillaceaeMicrobiotaHumansProbioticsSpecies SpecificityDNA Primers

Identifiers

PMID41760847
PMCPMC13049022

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.