Background: Infectious diseases cause significant production losses in aquaculture every year. Given the pivotal role played by the gut microbiota in regulating the host immune system, health and physiology, interest has risen in the possibility of controlling the fish health status by modulating the gut microbiota. An altered gut microbiota is often associated with a disease 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 the impact of formalin, a commonly used disinfectant in aquaculture, on the gut microbiome. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection and the subsequent formalin treatment.Results: We show that the distal gut of diseased salmon presented a different composition from that of healthy individuals, with an increased relative abundance of strains regarded as opportunistic in sick fish. Conversely, healthy salmon were dominated by a new, yet undescribed, Mycoplasma genus. We also observed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the treatment with formalin, while suited to resolve the external infection, was unable to recover the gut microbiota characteristic of healthy fish prior to treatment, potentially compromising the subsequent health status and growth performances of all treated fish.Conclusions: We conclude that infectious diseases have the potential of affecting the host gut microbiota at different body sites and that treatment optimization procedures should account for that. The formalin treatment is not an optimal solution from a holistic perspective, we suggest its coupling with a probiotic treatment aimed at re-establishing the original community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and growth performances and, while inviting further research on this microorganism, we also encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.