Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies

In this trial, rainbow trout with a body weight of 390.5 ± 36.8 g (mean ± standard deviation) and a standard length of 28.5 ± 0.8 cm were used. Since our purpose was to establish a microbial comparison regarding different methodological approaches, captivity fish were used, and reared under the following culture-controlled conditions, to avoid environmental factors which may have an impact on the fish microbiome (35). Fish were reared at IRTA la Ràpita (Spain) for 3 months under controlled water temperature, pH, and dissolved oxygen of 15.9 ± 0.7°C, 7.9 ± 0.2, and 8.8 ± 1.0 mg/L, in 450 L-tanks connected to an IRTAmar™ water recirculation system.