| Summary: | Fish are continuously exposed to a wide range of microorganisms present in the environment. This might influence the intestinal microbiota which in turn influence animal health and contribute to nutrition. Two turbot farms each with a different recirculating system concept were monitored. The objective of this study was to identify and compare in time the microbiota in (i) inflow water, (ii) water in the rearing tanks, (iii) feed and (iv) fish guts. In fish guts, a distinction was made between microbiota collected from faeces (lumen) and microbiota attached to the gut wall (mucus). Juvenile turbot, water and feed were sampled every 3 months over a 1-year period. Combined analyses using 16SrRNA gene PCR amplification and denaturing gradient gel electrophoresis (DGGE) and 16SrRNA gene pyrosequencing data showed that the microbial community composition in water changed over time and was farm-dependent. Microbial DGGE fingerprints clustered by farm suggesting a strong farm effect (Figure 1). Pyrosequencing data confirmed differences in microbiota in faeces, gut mucus, water and feed (Figure 2). The microbial community in turbot gut showed high inter-individual variation and was much less affected by system design or management. The turbot gut microbiota clustered based on the sampling location (lumen or mucus). The feed had the lowest bacterial diversity. Moreover, microbiota composition in water, feed, and gut were more or less stable over time during the observation period, suggesting that the gut was almost fully developed by the time the turbot reached 15g at the start of the experiment.
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