Fermentation of organisms for recycling is important for the efficient cycling of nitrogen and phosphorus resources for a sustainable society, but the functionality of fermented products needs to be evaluated. Here, we clarify the anti-pathogenic properties for fish of a compost-type feed additive fermented by thermophilic Bacillaceae using non-edible marine resources as raw materials. After prior administration of the compost extract to seabream as a fish model for 70 days, the mortality rate after 28 days of exposure to the fish pathogen Edwardsiella reached a maximum of 20%, although the rate was 60% without prior administration. Under such conditions, the serum complement activity of seabream increased, and the recovery time after anesthesia treatment was also fasten. Furthermore, texture and HSV analysis using field photos statistically visualized differences in the degree of smoothness and gloss of the fish body surface depending on the administration. These results suggest that thermophile-fermented compost is effective as a functional feed additive against fish disease infection, and that such soundness can be estimated by body surface analysis. This study provides a new perspective for the natural symbiosis industry, as well as for the utilization of field non-invasive diagnosis to efficiently estimate the quality of its production activities.