Intestinal microbiota of caged fish from the Adrtiatic Sea

In this study, the main goal was to explore quantitative and qualitative indices of the gut microbiota of two most important farmed fish, which experience similar environmental conditions and nutritionally similar diets. We identified the core gut microbiota and bacterial differences between the European bass (Dicentrarchus labrax) and gilt-head bream (Sparus aurata); farmed at the eight aquaculture sites along north to south of the Adriatic Sea coastline, Croatia. The investigated individuals were at pre-commercial size and reared in aquaculture cages, each cage having the density of 15 kg fish m-3. The diets fed to fish had nutritionally similar value among each aquaculture site to support optimal growth for each fish species, although each aquaculture site used differed feed brand, but the same feed for both species. DNA from the midgut of 10 individuals per fish from each aquaculture site were extracted for Illumina sequencing of the V3–V4 region of the bacterial 16S rRNA. A total of 1,428,925 raw reads were obtained from 15 samples included in the study. After the DADA2 process and filtering of the resulting table, 885,120 merged reads were obtained from 14 samples and a total of 195 amplicon sequence variants (ASVs) were identified at a similarity level of 99%.