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

## TL;DR

This study shows that analyzing saliva can reveal patterns in the upper gut microbiome linked to inflammation and pathogen presence, offering a noninvasive clinical tool.

## Contribution

A contamination-controlled protocol for profiling low-biomass uGI microbiota and identification of salivary microbiota types linked to inflammation and pathogen carriage.

## Key findings

- Two distinct salivary microbiota types were identified, one dominated by Prevotella 7, which was conserved in the duodenum.
- The Prevotella 7-dominated microbiota type was associated with lower opportunistic pathogen abundance and lower systemic TNF-α levels.
- Horizontal microbiota transfer was supported by transcriptional activity patterns in murine uGI tract.

## 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 Prevotella 7 genus – which were conserved in the duodenum. The Prevotella 7-dominated uGI microbiota type was associated with lower relative abundances of gastrointestinal and extraintestinal opportunistic pathogens. These patterns were reproducible in an independent cohort and associated with lower systemic TNF-α levels. Our findings suggest that noninvasive salivary microbiota profiling can stratify individuals based on uGI microbiota composition and inflammation-associated risk traits, offering new opportunities for clinical applications and translational studies.