The farming of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) is an important economic activity in many parts of the world. The optimal health and growth of these fish depend largely on their gut microbiota, a complex microbial ecosystem that plays crucial roles.
The gut microbiota, a complex ecosystem of microorganisms residing in the digestive tract, is increasingly recognized as a crucial player in animal health and well-being. For farmed salmonids, such as Atlantic salmon and rainbow trout, this microbial community is particularly important for optimal growth, robust health, and efficient physiology. However, until now, it has been difficult to compare and generalize the results of different studies on this topic due to variations in experimental designs, techniques, and bioinformatic analyses.
In this regard, scientists from the Swedish University of Agricultural Sciences and the University of Guelph (Canada) collected all publicly accessible 16S rRNA gene sequencing data with clearly established sample metadata from the intestinal content and mucosa of freshwater Atlantic salmon and rainbow trout sequenced on the Illumina MiSeq platform, to conduct a systematic meta-analysis of freshwater salmonid studies to determine the effect size and range of each technical, environmental, and host-associated factor influencing the gut microbiota, specifically alpha and beta diversities.
Introduction to Gut Microbiota
The term “microbiota” refers to the set of microorganisms, including bacteria, fungi, protozoa, and viruses, that reside in a specific environment. These microbes are crucial for the development and maintenance of various physiological functions in their eukaryotic hosts, including humans and other animals. Within the gastrointestinal tract of animals, the gut microbiota plays a fundamental role in nutrient absorption, metabolism, aging, immune system regulation, and protection against pathogen invasion.
Factors Influencing Gut Microbiota
Microbial communities in the gut are influenced by a wide variety of environmental and host factors:
- Host Factors: Developmental stage, health conditions, and species.
- Environmental Factors: Temperature, light, and diet.
A Systematic Approach: The Meta-analysis
Most fish microbiota studies typically investigate one or two factors while controlling for several others, making it difficult to compare results across studies due to variations in technical factors (such as DNA extraction, PCR, and bioinformatics methods).
To address these limitations, the research team conducted a meta-analysis, a rigorous methodology that allows for the combination of results from multiple studies. The goal was to identify and rank the technical, environmental, and host factors impacting the microbial diversity of the gut in freshwater salmon and trout.
The analysis included 16S rRNA gene sequencing data from 783 samples from 19 studies. Advanced bioinformatics tools were used to identify patterns and trends in microbial composition.
Key Findings: Factors Shaping the Salmonid Gut Microbiome
The study revealed that a multitude of factors significantly affect the diversity and composition of the gut microbiota in salmonids.
Technical Factors: DNA Extraction Kit and Target Region
These technical elements were found to significantly affect the beta diversity of the gut microbiota. Beta diversity refers to differences in microbial communities between different environments or samples. The choice of target region for sequencing and the DNA extraction kit used can lead to variations in the microbial populations detected.
Environmental and Host-associated Factors: Diet and Initial Fish Weight
These factors had a more pronounced impact on alpha diversity, which measures diversity within a single sample. The diet of the fish and their initial weight were crucial in shaping the microbial diversity within their guts.
Comparative Insights: Salmon vs. Trout
The analysis revealed clear differences between the gut microbiota of Atlantic salmon and rainbow trout:
- Atlantic Salmon: Exhibited higher alpha diversity, indicating a more diverse microbial community within individual fish. They also had higher abundances of Enterococcus and Staphylococcus.
- Rainbow Trout: Showed a greater presence of Weissella and Mycoplasma, but a lower overall alpha diversity compared to salmon.
Implications for Salmonid Aquaculture
These findings have significant implications for the salmonid aquaculture industry. By understanding the factors influencing the gut microbiota of salmonids, researchers and aquaculturists can develop strategies to optimize the health and productivity of the fish. For instance, standardizing experimental methods and carefully considering environmental conditions will be essential for obtaining reliable and comparable results. Additionally, identifying specific bacterial groups associated with different fish species can inform targeted interventions to improve gut health.
Conclusion
The findings from this meta-analysis fill a critical knowledge gap in our understanding of salmonid gut microbiota. Standardizing technical methodologies and considering environmental and host factors are essential for future research. This comprehensive approach will pave the way for more consistent and reliable studies, contributing to the optimal growth and health of these economically important fish species.
The knowledge generated by this meta-analysis represents a fundamental step in unraveling the secrets of the gut microbiome of salmon and trout. This information can be invaluable for developing management and feeding strategies that promote the health and well-being of these fish, with positive implications for the sustainability of aquaculture.
The study was funded by the Swedish Research Council and the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS).
Contact
David Huyben
Department of Animal Biosciences, University of Guelph
Guelph, Canada.
Email: huybend@uoguelph.ca
Reference (open access)
Cao, S., Dicksved, J., Lundh, T., Vidakovic, A., Norouzitallab, P., & Huyben, D. A meta-analysis revealing the technical, environmental, and host-associated factors that shape the gut microbiota of Atlantic salmon and rainbow trout. Reviews in Aquaculture. https://doi.org/10.1111/raq.12913
