Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals

Abstract

Background Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection due to a natural outbreak and the subsequent formalin treatment. Results We identified Tenacibaculum dicentrarchi as the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed, Mycoplasma genus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance of Aliivibrio sp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones. Conclusions We conclude that external Tenacibaculum infections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establish a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and growth performances, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.

Microbiota in intestinal digesta of Atlantic salmon (Salmo salar), observed from late freshwater stage until one year in seawater, and effects of functional ingredients: a case study from a commercial sized research site in the Arctic region

“…As the Atlantic salmon progressed towards the adult stage, the enrichment of genus Mycoplasma at SW2 and SW3 time points compared to FW and SW1 was one of the most prominent differences found in our study, possibly indicating that the host is a determinant for microbial assemblage by attracting specific bacterial communities depending on the developmental stage of the fish [ 53 , 54 ]. Previous studies have found Mycoplasma , a member of the core microbiota, to be one of the most abundant bacteria in farmed as well as wild Atlantic salmon during seawater stages [ 26 , 55 – 59 ] reaching levels above 70% of total abundance in certain cases [ 19 , 45 , 58 ].…”

“…For example, Mycoplasma abundance was strongly associated with flesh color darkness, suggesting a role in the production of carotenoids [ 60 ]. Moreover, the Mycoplasma has shown ecological and functional associations with the host [ 61 ] and is positively correlated with body weight [ 54 ]. However, the present study did not show a significant association between the relative abundance of Mycoplasma and the observed host responses.…”

Key Drivers of Ecological Assembly in the Hindgut of Atlantic Cod (Gadus morhua) when Fed with a Macroalgal Supplemented diet – How Robust Is the Gut to Taxonomic Perturbation?

“…The fish gut microbiome is essential to systemic function, fish health 37 , immune support 38 and digestive capacity 39 . However, the factors that govern the microbial community colonisation, assembly, and succession in fish species are poorly understood, in terms of both the ecological assembly mechanisms and development within the life cycle.…”

Prebiotics Modify Host Metabolism in Rainbow Trout (Oncorhynchus Mykiss) Fed with a Total Plant-Based Diet: Potential Implications for Microbiome-Mediated Diet Optimization

“…Indeed, uorescent in situ hybridization suggested that salmonid strains of Mycoplasma are intracellular [52]. The absence of pathogenicity genes in the salmonid strains [51] suggests a mutually bene cial relationship, as observed in the hadal sail sh, where the Mycoplasma is bene cial to the host by providing biotin in a nutrient-poor environment [53] and aiding in host defence [53,54]. In the present study, we observed 2 OTUs belonging to the genus Mycoplasma and they were differentially abundant in all feeding groups (except the inulin2 group).…”