Exploring the metagenomic data of both wild and farmed Atlantic Salmon and Sea Bream within CIRCLES project

Presentation from the Research Group for Genomic Epidemiology – 11 September 2023

Aquaculture is a crucial global food system, however contemporary food systems are faced with efficiency and sustainability challenges. The CIRCLES project aims to enhance food system sustainability and safety, with work project 7 lead by DTU exploring the metagenomic data of both wild and farmed Atlantic Salmon and Sea Bream. The focus is to characterize their resistomes and microbiomes and to understand the antimicrobial resistance (AMR) patterns and differences between fish and the environment.

Mapping metagenomic data of 307 Atlantic Salmon and 217 Sea Bream samples against reference databases using k-mer alignment (KMA), characterization of the resistome and microbiome revealed patterns where AMR was found to be higher in fish samples although with a lower diversity than the environment. Additionally, the total AMR load was found to be higher for wild fish compared to their farmed counterparts. The environmental and fish microbiomes contained several genera typical of cold saline aquatic settings, with the fish displaying reduced diversity relative to the environment.
The next step of the CIRCLES metagenomics analysis involves sequencing an additional 500-600 samples from the intervention phase of the project, in which probiotics were administered to the fish. The goal is to discern the changes in the fish's microbiome and resistome before and after introducing probiotics to determine any significant changes.

Eventually, the hope is to be able to introduce "Smart Microbiome Modulators" (SMM's) such as probiotics to aquaculture and other food systems, in order to increase both efficiency and sustainability of the production.

Frederik Duus Møller’s presentation