Introduction
The microbiome is increasingly recognised as a key determinant of fish health ; however, its functional role in aquaculture species remains poorly resolved, limiting translation into practice . In this study, we examined the effect of early-life microbial conditioning on microbiome development and stability and fish performance under stress later in life. Germ-free rainbow trout (Oncorhynchus mykiss) eyed stage (~200 degree-days post-fertilisation) eggs were exposed to one of three microbial environments: (1) clean water with low microbial abundance, (2) water representative of conventional recirculating aquaculture systems (RAS), and (3) water inoculated with faeces from healthy adult rainbow trout. Hatched fish were reared under these conditions through the early developmental stages and subsequently subjected to chronic stress (e.g. high stocking density) at the juvenile stage (~5–10 g). Microbiome diversity, succession, and stability was characterised using Oxford Nanopore sequencing of the 16S rRNA gene across key developmental milestones. Host responses were quantified through growth performance, survival, and welfare indicators, alongside continuous monitoring of water quality and system microbial dynamics.
Results & Discussion
This work will establish whether targeted manipulation of early-life microbial environments can shape microbiome stability and enhance host resilience to chronic stress. The findings are expected to inform the development of early-life microbial interventions to improve robustness, reduce disease risk, and support sustainable intensification of aquaculture systems.
References
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