Nanopore-Based Metagenomic Approaches for Detection of Bacterial Pathogens in Recirculating Aquaculture Systems

Abstract

The microbial community in a recirculating aquaculture system (RAS) is pivotal in fish health, contributing significantly to the productive performance during the growing-out phase. Classical and molecular methods using PCR for species-specific amplifications have traditionally been used for bacterial community surveillance. Unfortunately, these approaches mask the real bacterial diversity and abundance, population dynamics, and prevalence of pathogenic bacteria. In this study, we explored the use of Oxford Nanopore Technology to characterize the microbiota and functional metagenomics in a commercial freshwater RAS. Intestine samples from Atlantic salmon (Salmo salar (85 ± 5.7 g)) and water samples from the inlet/outlet water, settling tank, and biofilters were collected. The full-length 16S rRNA gene was sequenced to reconstruct the microbial community, and bioinformatic tools were applied to estimate the functional potential in the RAS and fish microbiota. The analysis showed that bacteria involved in denitrification processes were found in water samples, as well as metabolic pathways related to hydrogen sulfide metabolism. Observations suggested that fish classified as sick exhibited decreased microbial diversity compared with fish without clinical symptomatology (p

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