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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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s42523-021-00096-2.

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