Long-term intermittent exposure to fluoride and tebuconazole alters gill, skin and gut microbiomes in rainbow trout (Oncorhynchus mykiss)
4 affiliations
- 1Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac, F-33600 France
- 2Ploufragan-Plouzané-Niort Laboratory, VIMEP Unit, INR Emerg’In, Plouzané, 29280 France
- 3Centre for Organismal Studies, Aquatic Ecology and Toxicology, University of Heidelberg, Heidelberg, Germany
- 4INRAE UMR BIOGECO 1202, Domaine de l’Hermitage, 69 route d’Arcachon, CS 80227, Cestas, 33612 France
Abstract
Background: Fluoride and tebuconazole are two compounds widely used in industrial processes and agriculture, respectively, and are regularly detected in surface waters. Therefore, there is an urgent need to characterise their effects on aquatic organisms. In this context, adopting a holistic approach that integrates the host and its associated microbiomes, the holobiont, is particularly relevant. In this study, rainbow trout were exposed from 6 days post-fertilisation for 7 months to a daily 7-hour pulsed regime of two concentrations of fluoride (6.8 or 24.7 mg/L, representing environmentally relevant levels for contaminated hotspots), to tebuconazole (51.7 µg/L, within the range of agricultural runoff peaks), or maintained in control conditions. At the end of the exposure period, gill, skin and intestine microbiomes were characterized using 16 S rRNA gene metabarcoding.
Results: Fluoride and tebuconazole significantly affected the bacterial alpha diversity in gill and skin tissues. Beta diversity was significantly affected in gill and skin tissues, whereas the intestine exhibited a weak overall treatment effect without significant pairwise differences. If compared to the control treatment, fluoride exposure altered microbial co-occurrence networks, affecting bacterial interconnections in a tissue-specific manner, with reduced interconnections in gills and increased interconnections in skin and intestine compared to the control treatment. Shifts in taxonomical composition were present following exposure to both pollutants, and notably increases in the relative abundance of fish pathogens such as Candidatus Piscichlamydia, Flavobacterium and Aeromonas were observed. Increased abundance of Aeromonas (gill, skin and intestine) and Acidovorax (gill), along with functional predictions, suggested potential alterations in pathways related to antibiotic resistance, warranting further metagenomic investigation.
Conclusions: These results highlight alterations of gill, skin and intestine microbiomes in the rainbow trout following chronic exposure to fluoride and tebuconazole, with distinct and tissue-specific microbial responses. Beyond taxonomical shifts, the observed alterations of bacterial co-occurrence networks, enrichment of pathogenic bacteria, and antibiotic-resistant taxa, indicating that the fish microbiome is a sensitive bioindicator of chronical chemical stress. Whether these microbial shifts translate into adverse host health outcomes remains to be investigated in future studies.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05492-9.
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BibTeX
@article{suchet2026longterm,
title = {{Long-term intermittent exposure to fluoride and tebuconazole alters gill, skin and gut microbiomes in rainbow trout (Oncorhynchus mykiss)}},
author = {Marine Suchet and Pauline Pannetier and Morgane Danion and Thomas Braunbeck and Préscillia Alves Gomes and Jérôme Cachot and Laure Bellec},
journal = {BMC Microbiology},
year = {2026},
month = aug,
doi = {10.1186/s12866-026-05492-9},
url = {https://doi.org/10.1186/s12866-026-05492-9},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Long-term intermittent exposure to fluoride and tebuconazole alters gill, skin and gut microbiomes in rainbow trout (Oncorhynchus mykiss)
AU - Marine Suchet
AU - Pauline Pannetier
AU - Morgane Danion
AU - Thomas Braunbeck
AU - Préscillia Alves Gomes
AU - Jérôme Cachot
AU - Laure Bellec
PY - 2026
DA - 2026/08/06
JO - BMC Microbiology
DO - 10.1186/s12866-026-05492-9
UR - https://doi.org/10.1186/s12866-026-05492-9
AB - Background: Fluoride and tebuconazole are two compounds widely used in industrial processes and agriculture, respectively, and are regularly detected in surface waters. Therefore, there is an urgent need to characterise their effects on aquatic organisms. In this context, adopting a holistic approach that integrates the host and its associated microbiomes, the holobiont, is particularly relevant. In this study, rainbow trout were exposed from 6 days post-fertilisation for 7 months to a daily 7-hour pulsed regime of two concentrations of fluoride (6.8 or 24.7 mg/L, representing environmentally relevant levels for contaminated hotspots), to tebuconazole (51.7 µg/L, within the range of agricultural runoff peaks), or maintained in control conditions. At the end of the exposure period, gill, skin and intestine microbiomes were characterized using 16 S rRNA gene metabarcoding. Results: Fluoride and tebuconazole significantly affected the bacterial alpha diversity in gill and skin tissues. Beta diversity was significantly affected in gill and skin tissues, whereas the intestine exhibited a weak overall treatment effect without significant pairwise differences. If compared to the control treatment, fluoride exposure altered microbial co-occurrence networks, affecting bacterial interconnections in a tissue-specific manner, with reduced interconnections in gills and increased interconnections in skin and intestine compared to the control treatment. Shifts in taxonomical composition were present following exposure to both pollutants, and notably increases in the relative abundance of fish pathogens such as Candidatus Piscichlamydia, Flavobacterium and Aeromonas were observed. Increased abundance of Aeromonas (gill, skin and intestine) and Acidovorax (gill), along with functional predictions, suggested potential alterations in pathways related to antibiotic resistance, warranting further metagenomic investigation. Conclusions: These results highlight alterations of gill, skin and intestine microbiomes in the rainbow trout following chronic exposure to fluoride and tebuconazole, with distinct and tissue-specific microbial responses. Beyond taxonomical shifts, the observed alterations of bacterial co-occurrence networks, enrichment of pathogenic bacteria, and antibiotic-resistant taxa, indicating that the fish microbiome is a sensitive bioindicator of chronical chemical stress. Whether these microbial shifts translate into adverse host health outcomes remains to be investigated in future studies. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05492-9.
SN - 1471-2180
ER -