Study-specific factors constitute the largest explanatory driver of variation in the salmonid gill microbiome, followed by rearing system and host species, according to a meta-analysis led by Wouter Mes, Marnix Gorissen, and Maartje A. H. J. van Kessel published in Animal Microbiome. Analyzing the relative contributions of environmental, host-associated, and technical factors across publicly available datasets, the researchers found that no other investigated factors significantly accounted for the observed variation.
The investigation evaluated 20 studies encompassing 804 high-quality gill samples from Atlantic salmon, rainbow trout, and Arctic charr. The team reanalyzed these datasets to assess which factors significantly explained microbial community variation and to identify specific microbial genera linked to particular environmental and host conditions within aquaculture settings.
To identify gill-specific microbial signatures that persist across disparate studies, the researchers followed their initial evaluation with an analysis comparing 400 gill samples and environmental samples.
Across the reanalyzed studies, the presence of disease was associated with a statistically significant reduction in microbial diversity and richness on the gills. Despite the prominence of study-specific variation, the fish shared multiple core microbial genera across rearing systems, including beneficial bacteria involved in the nitrogen cycle.
Gill health represents a major issue in aquaculture, making the functional role of the gill microbiome in salmonid health an expanding research topic. Establishing how these microbial communities contribute to fish health requires resolving the relative importance of environmental conditions and fish-associated factors in shaping the gill microbiota, while explicitly accounting for technical variables such as sampling methods and DNA extraction methods.
To establish the role of gill microbiota in salmonid health, the meta-analysis evaluated the relative contributions of environmental factors, fish-associated factors, and technical variables across all publicly available salmonid gill microbiome studies. The dataset compiled for this reanalysis encompassed twenty studies containing 804 high-quality gill samples from Atlantic salmon, rainbow trout, and Arctic charr. By reanalyzing these datasets, the researchers sought to determine which factors significantly explained microbial community variation and which genera of microorganisms are associated with specific factors. Following this initial assessment, the authors conducted an analysis of 400 gill- and environmental samples to identify gill-specific microbial signatures across studies.
The investigation revealed that study-specific factors represent the largest explanatory factor for the salmonid gill microbiome, followed in significance by the rearing system and the fish species. In contrast, no other investigated factors significantly explained variation across the examined datasets. When evaluating health status across studies, the presence of disease led to a significantly reduced microbial diversity among the fish. Specifically, the authors identified a reduced microbial richness as a shared signature of disease across salmonid gill microbiota, confirming a consistent pattern in affected populations across the evaluated literature.
Despite most variation arising from study-specific effects, the researchers found that salmonids share multiple core genera across studies. These shared groups include beneficial nitrogen-cycle bacteria, which were widespread throughout all rearing systems evaluated in the meta-analysis.
These findings support the need for more standardized sampling and extraction methods in salmonid research to minimize study-specific factors when searching for biomarkers of health or disease. Even with study-specific factors driving the majority of community variation, the meta-analysis demonstrates that shared signatures for disease, characterized by reduced microbial richness, and potential beneficial microorganisms can be successfully identified across salmonid gill microbiota.
Subject of Research: Factors determining salmonid gill microbiome variation in aquaculture
Article Title: Environmental and host-associated factors are the main determining factors for the salmonid gill microbiome
Article References: Mes, W., Gorissen, M., & van Kessel, M. A. H. J. (2026). Environmental and host-associated factors are the main determining factors for the salmonid gill microbiome. Animal Microbiome. https://doi.org/10.1186/s42523-026-00624-y
Image Credits: AI Generated
DOI: 10.1186/s42523-026-00624-y
Keywords: salmonid gill microbiome, Atlantic salmon, rainbow trout, Arctic charr, aquaculture, microbial diversity, meta-analysis, nitrogen-cycle bacteria, Environmental, host-associated, factors, main
