Skin Microbiota of Salmonids: A Procedure to Examine Active Bacterial Populations Using an RNA-Based Approach

Fish microbiota studies have mostly addressed intestinal bacterial communities because of their role in fish physiology; however, the skin has been studied less despite its as first pathogen barrier host. DNA-based molecular techniques contributed to improving our understanding microbiota, but this approach faces challenges, such low count bacteria healthy skin. To overcome limitation, an RNA-based was developed study salmonids, including tissue sampling, RNA extraction, and downstream procedures obtain PCR amplicons for next-generation sequencing. The protocol originated work overcomes limitations counts is useful describing active application salmonids reared both experimental setting on a farm revealed that trout dominated by from phylum Proteobacteria (>65%). At genus level, Piscirickettsia (46%) highlighted most abundant unit samples; contrast, Pseudoalteromonas (26%), followed Escherichia_Shigella (~25%), farmed trout.