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 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-establishing a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.

Microbiome “Inception”: an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host

“…Overall, the salmon gut mucosa was dominated by the genus Mycoplasma ( Fig. 1B ), a known commensal of the salmon intestinal microbiome ( 9 , 34 – 38 ). However, there was evidence that the gut microbiota differed between uninfected and infected individuals.…”

Efficacy of Utilization of All-Plant-Based and Commercial Low-Fishmeal Feeds in Two Divergently Selected Strains of Rainbow Trout (Oncorhynchus mykiss): Focus on Growth Performance, Whole-Body Proximate Composition, and Intestinal Microbiome

“…Accordingly, it has recently been suggested that Mycoplasma , due to its dominance in the distal intestine of rainbow trout and other farmed salmonids, could have a mutualistic relationship with its host ( Rasmussen et al, 2021 ). In Atlantic salmon ( Salmo salar ), the abundance of Mycoplasma has positively been associated with improved growth, carotenoid utilization, and disease resilience of the host ( Bozzi et al, 2021 ). In addition, this genus harbors genes for long-chain polymer degradation, such as chitin, which is particularly abundant in insects, that are part of the natural diet of juvenile salmonids.…”

Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet

“…The fish gut microbiome is essential to systemic function, fish health 44 , immune support 45 , and digestive capacity 46 . 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.…”