Community Level Physiological Profiles (CLPP) is novel method to evaluate microbial activity and diversity in ecosystems. According to the previous findings, poly-β-hydroxybutyrate (PHB) as a bio-control product, increases bacterial diversity in some aquatic animals. In this study, the effects of four experimental diets (control, combination of two PHB degrading bacteria, 2% PHB, bacteria+ 2% PHB) on the anaerobic activity of cultivable bacteria in Siberian sturgeon fingerlings hindgut was investigated. Community level physiological profile (CLPP) was used to analyze anaerobic metabolism by using Biolog™ Ecoplate microplates. The results indicated that anaerobic metabolic potential of the bacterial community was different in the 2% PHB-treated fishes as compared with other groups and PHB improved anaerobic metabolism of bacteria in fingerlings. Also anaerobic metabolism of bacteria was calculated on the different carbon sources (amino acids, carboxylic acids, carbohydrates and polymers) in Ecoplate microplates and the results showed that fish treated with PHB had the highest metabolic activity in mentioned carbon sources. The results of this research revealed that replacing of the diets with 2% PHB increases anaerobic metabolism of culturable bacteria in Siberian sturgeon hindgut while adding PHB degrading bacteria did not change this parameter in fingerlings.