Microbial profiles of Alaskan rainbow trout from 16S rRNA amplicon data

Rainbow trout (Oncorhynchus mykiss) is a higly valued aquaculture species that belongs in the Salmonidae family, native only to the North Pacific. This study explores the microbiome composition of the intestinal tract of 20 wild-caught rainbow trout specimens collected in the Wood River system of southwest Alaska. Utilizing the Illumina NovaSeq 6000 platform, we sequenced the targeted 16S rRNA gene (V3-V4 region). After initial filtering the reads were analyzed using the DADA2 pipeline, resulting in Amplicon Sequencing Variants (ASVs), which were then taxonomically classified. This study constitutes a fundamental analysis on the gut ecosystem in wild rainbow trout with valuable insights that could inform strategies for improving the welfare and sustainability of cultured populations.