PacBio Sequencing for Full-Length 16S rRNA Gene Classification of Bacteria Communities in Aquaculture Production of Atlantic Salmon

Understanding fish-microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community accommodating the rearing systems and fish surfaces. Accurate methods to generate and analyse these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. The purpose of this study was to demonstrate the advantages of using PacBio circular consensus sequencing technology in microbial community studies. This is the first study that capture full-length 16S rRNA gene sequences from Atlantic salmon. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Comparisons with 16S rRNA gene assignments showed that culturability in this study was remarkably high (~44%), and that there is a lack of properly defined bacterial species associated to Atlantic salmon. Our data demonstrate that full-length 16S rRNA sequences has the potential to improve the phylogenetic resolution and insight for under-characterized microbial environments and become a helpful tool for a more precise microbial community profiling of Atlantic salmon.