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Early life stress causes persistent impacts on the microbiome of Atlantic salmon
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume: 40, Start page: 100888
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Farmed fish are commonly exposed to stress in intensive aquaculture systems, often leading to immune impairment and increased susceptibility to disease. As microbial communities associated with the gut and skin are vital to host health and disease resilience, disruption of microbiome integrity could...
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Farmed fish are commonly exposed to stress in intensive aquaculture systems, often leading to immune impairment and increased susceptibility to disease. As microbial communities associated with the gut and skin are vital to host health and disease resilience, disruption of microbiome integrity could contribute to the adverse consequences of stress exposure. Little is known about how stress affects the fish microbiome, especially during sensitive early life stages when initial colonisation and proliferation of host-associated microbial communities take place. Therefore, we compared the effects of two aquaculture-relevant early-life stressors on the gut and skin microbiome of Atlantic salmon fry (four months post hatching) using 16S rRNA amplicon sequencing. Acute cold stress applied during late embryogenesis had a pronounced, lasting effect on the structure of the skin microbiome, as well as a less consistent effect on the gut microbiome. Follow-up targeted qPCR assays suggested that this is likely due to disruption of the egg shell microbial communities at the initial stages of microbiome colonisation, with persistent effects on community structure. In contrast, chronic post hatching stress altered the structure of the gut microbiome, but not that of the skin. Both types of stress promoted similar Gammaproteobacteria ASVs, particularly within the genera Acinetobacter and Aeromonas, which include several important opportunistic fish pathogens. Our results demonstrate the sensitivity of the salmon microbiome to environmental stressors during early life, with potential associated health impacts on the host. We also identified common signatures of stress in the salmon microbiome, which may represent useful microbial stress biomarkers.
Microbiota; Temperature; Cold shock; Salmo salar; Aquaculture
Faculty of Science and Engineering
This work was funded by a BBSRC-NERC, United Kingdom Aqua-culture grant (BB/M026469/1), the Welsh Government and Higher Education Funding Council for Wales (HEFCW) through the Sˆer Cymru National Research Network for Low Carbon Energy and Environment (NRN-LCEE) AQUAWALES project to SC, and the European Regional Development Fund via WEFO and the SMARTAQUA Operation to CGL.