# Metabolomic fingerprinting of soft tissues uncovers taxonomic, physiological, and ecological aspects of river fishes

## TL;DR

This study uses metabolomics to analyze fish tissues and reveals how environmental stress from cyanobacteria affects fish in French rivers.

## Contribution

The study demonstrates the use of tissue-specific metabolomics to detect ecological stress in fish linked to cyanobacterial blooms.

## Key findings

- Muscle tissues showed the most distinct species differentiation in metabolomic profiles.
- Fish from the Vienne river exhibited signs of metabolic stress, including elevated oxidized glutathione and bile acids.
- Environmental metabolomics can serve as a sensitive tool for ecological monitoring and bio-indication.

## Abstract

Recent advances in molecular phenotyping have driven the rapid growth of untargeted, multi-dimensional approaches such as epigenomics, transcriptomics, proteomics, and metabolomics. When applied to ecology, these high-throughput omics tools offer powerful new molecular trait descriptors for investigating biological and environmental processes. Using UHPLC-HRMS/MS, we analyzed metabolome variations in gut, liver, and muscle tissues of chubs and gudgeons collected in summer 2019 from French rivers affected by benthic cyanobacterial blooms. Tissue-specific metabolomic profiles were evident, with muscle metabolomes showing the most distinct species differentiation. The different tissue metabolomes of both fish species also varied by sampling location, indicating local environmental influences. Notably, fish from the Vienne site exhibited molecular signatures of metabolic stress, including elevated oxidized glutathione and bile acids, and decreased purines, amino acids, peptides, and lipids—potentially linked to anatoxin-a-producing cyanobacterial mats. These findings underscore the potential of environmental metabolomics as a sensitive tool for assessing ecological stress and support its integration into routine environmental bio-indicator programs.

The online version contains supplementary material available at 10.1007/s10695-026-01638-8.

LC-HRMS-based metabolomics on guts, livers, and muscles of fish from the Loire, Vienne, and Cher rivers.Metabolomes of both chubs and gudgeons exhibit a similar relation to local environmental conditions.Metabolites discriminating the different metabotypes were identified and suggest a stress response in fish from river Vienne.Muscle metabolomes exhibit an even more discriminant signature than liver or gut.

LC-HRMS-based metabolomics on guts, livers, and muscles of fish from the Loire, Vienne, and Cher rivers.

Metabolomes of both chubs and gudgeons exhibit a similar relation to local environmental conditions.

Metabolites discriminating the different metabotypes were identified and suggest a stress response in fish from river Vienne.

Muscle metabolomes exhibit an even more discriminant signature than liver or gut.

The online version contains supplementary material available at 10.1007/s10695-026-01638-8.