Microorganisms are key members of the ecosystems: they provide essential nutrients to entire food webs, recycle waste products, and form protective layers on and in larger organisms that assist their host in a multitude of physiological functions . Gut microbiome plays a critical role in different aspects of fish biology ; through direct involvement in the digest ive process by providing the nutrients and minerals needed for the fish, or its active role in immune response and barrier function with major consequences for the fish health and welfare. However, studies on marine food-associated microbiomes are far behind current state-of-the-art research in terrestrial agriculture and humans. According to the Norwegian Veterinary Institute, infectious diseases in sea cages account for one of the most important causes of economic loss in th e salmon farming industry. Notably, f armed salmon are known to be less resilient compared to the wild salmon and, in particular , smolts experience extreme stress and challenges when they are transferred from recirculating aquaculture facilities on land to sea cages where the conditions are much less controlled and where they are exposed to an array of pathogens. Consequently, m ortality following sea transfer is one of the major culprits for economic loss and impaired animal welfare in the salmon farming industry. The fish microbiota is also known to changes as the fish moves to this new marine environment. Investigating the differences between the gut microbiome of wild versus farmed smolts will improve our understanding of an important yet understudied aspect of the adaptation of salmon smolts to marine conditions and shed light on this critical transitional stage. Therefore, as part of the project BlueRemediomics, we sampled the posterior intestine and feces of salmon one week after sea-transfer from land-based flowthrough aquaculture system as well as smolts of comparable size in the wild. Total genomic DNA was extracted and destined for sequencing by both a metagenomics and metataxonomic approach. For metataxonomic, DNA amplicon libraries were generated targeting the V3-V4 regions (341F/R805) of the 16S rRNA gene and the sequencing was performed on the Illumina platform. For metagenomic, samples with good quality for library preparation were sequenced also with the Illumina platform, obtaining around of 10M reads per library. Analysis of the sequences was performed following standards pipelines for metataxonomic and metagenomic analysis. Briefly, clean sequences chimeric detection and deletion, followed by Amplicon Sequence Variant (ASV) assignment were completed using DADA2 plugin. Taxonomy was assigned at a 99% similarity level using the q2- feature-classifier plugin with the SILVA 138 database. Composition of the gut microbiota between the fish recently transferred to seawater after land-based flowthrough aquaculture system and the wild smolts, shed light on the differential role of rearing environments on gut microbiota , pav ing the way to improve the performance and welfare of farmed salmon.
Acknowledgments: Funding: BlueRemediomics -Grant No.101082304, EU Horizon Europe Programme. Farmed fish were sampled from Lerøy´s land and sea facilities in Norway.