Introduction
The assembly of the gut microbiome in fish is a dynamic and tightly regulated process influenced by host genetics, early-life environmental exposure, diet, and aquaculture practices. Although, the host-focused RNA-seq datasets are routinely generated in aquaculture research and breeding programs yet the microbial information contained in unmapped reads is typically overlooked. Advances in high-throughput sequencing technologies, along with the multi-omics approaches has enabled integration of microbial community structure with the functional characterization. This combined approach provides insights into microbial roles and will improve understanding host-microbiome-environment interactions and aquaculture sustainability. This study aims to comprehensively characterize the intestinal meta-transcriptome of Oncorhynchus mykiss using different rearing systems, with particular emphasis on the influence of early-life rearing environments.
Materials and Methods
Eyed eggs (200 degree-days post fertilization) of specific pathogen-free (SPF) rainbow trout (Oncorhynchus mykiss) were reared in two contrasting systems flow through system (FTS: low organic matter) and Recirculatory Aquaculture System (RAS: high organic matter), each in triplicates. At late fry stage (35 days post hatching, dph) the gut samples were collected along with corresponding water microbiome samples via vacuum filtration using membrane filters (0.22 μm nitrocellulose membrane filter, 47 mm diameter, MilliporeTM). Total DNA and RNA was extracted from both the sample types. Microbial community composition will be characterized using 16S rRNA gene amplicon sequencing to study the influence of rearing conditions on the microbiome assembly. Furthermore, meta-transcriptomic analysis of gut-associated microbial communities and water samples was conducted by RNA-seq datasets. These poly(A)-selected RNA-seq enriched for eukaryotic mRNA, enable retrospective investigation of microbial functional dynamics under various baseline conditions. Relevant datasets will be identified using targeted keywords including "rainbow trout" and "Oncorhynchus mykiss", "fish gut microbiota", "microbial dysbiosis fish" along with the study type "gut meta-transcriptome". Paired-end reads will be processed using standardized bioinformatics pipelines incorporating automatic library type detection, quality control, and validation of read mappings.
Expected Results
It is expected that microbial community in the two rearing systems vary significantly in both water and gut. The RAS with more stable water microbiota will support a more stable microbiota with higher alpha diversities. In contrast, the FTS with continuous water exchange harbor less stable microbial community often dominated by potentially pathogenic r-strategists indicating, including opportunistic or pathogenic taxa. These differences in environmental microbial composition are expected to directly influence initial gut colonization and subsequent microbiome assembly in rainbow trout.
Discussion
Early-life rearing conditions are known to significantly influence the microbial community assembly in both water and gut environments of fish. FTS and RAS previously showed differences in the water microbial community due to the differences in water exchange. In addition, the bacterial density in water entering the rearing tanks of RAS was shown to be more than 10 times higher than in the FTS. It is expected that early environmental microbial conditions will have lasting impacts on both microbial functional potential and host intestinal health.
Overall, it is anticipated that aquaculture system design plays a central role in shaping microbiome- development and resilience in fish, supporting the concept that early microbial environments have long-term implications for aquaculture and productivity.
Acknowledgement
This work is supported by the Austrian Science Fund (FWF) as part of the Horizon Europe initiative "European Partnership on Animal Health & Welfare" under the AQUAWELL project (FA40125002).