Evidence map›Paper›PMID 40746257›Full record

ArticleGut microbes2025

Contamination-controlled upper gastrointestinal microbiota profiling reveals salivary-duodenal community types linked to opportunistic pathogen carriage and inflammation.

Nina S Schmidt, Elisabeth Dörner, Daniel Podlesny, Elisabeth Bohlhammer, Alena M Bubeck, Hannah K Ruple, Vivian Tetzlaff-Lelleck, Christian Sina, Herbert Schmidt, W Florian Fricke

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Article in Gut microbes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Complete genomes of 12Microbiology resource announcements · 2026
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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

10 authors.

Nina S SchmidtDepartment of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
Elisabeth DörnerDepartment of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
Daniel PodlesnyDepartment of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
Elisabeth BohlhammerDepartment of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
Alena M BubeckDepartment of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
Hannah K RupleDepartment of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.
Vivian Tetzlaff-LelleckInstitute of Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany.
Christian SinaInstitute of Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany.
Herbert SchmidtDepartment of Food Microbiology and Hygiene, University of Hohenheim, Stuttgart, Germany.
W Florian FrickeDepartment of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The upper gastrointestinal (uGI) microbiota has been implicated in infectious, metabolic, and immunological conditions, yet remains poorly characterized due to invasive sampling and low microbial biomass. We developed and validated a contamination-controlled 16S rRNA gene and transcript-based protocol to profile the murine and human uGI microbiota from low-biomass samples. We applied this protocol to murine esophageal, gastric, and duodenal tissues, and to human saliva, gastric, and duodenal aspirates from patients undergoing endoscopy for suspected food-related, mild GI symptoms. Our objective was to identify conserved compositional and structural uGI microbiota patterns and assess their clinical relevance in relation to pathogen burden and inflammation. In mice, we found evidence for transcriptionally inactive and active intestinal taxa along the uGI tract, supporting horizontal microbiota transfer. In humans, we identified two distinct, inversely correlated salivary microbiota types - one dominated by the

Indexed as

BacteriaDuodenumGastrointestinal MicrobiomeInflammationSalivaUpper Gastrointestinal TractAdultAnimalsFemaleHumansMaleMiceMice, Inbred C57BLMiddle AgedRNA, Ribosomal, 16SRNA, Ribosomal, 16Scontaminationduodenumdysbiosisextraintestinal infectionshuman microbiotamicrobiota transfermicrobiota typesmouse microbiotaSalivaupper gastrointestinal tract microbiota

Identifiers

PMID40746257
PMCPMC12320837

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Registered trials

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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.