Relationships between the Gut Microbiota of Juvenile Black Sea Bream (Acanthopagrus schlegelii) and Associated Environment Compartments in Different Habitats

The fish-gut microbiota play a key role in the physiology, development, and fitness of its host. An understanding of fish-gut microbial communities and the factors influencing community composition is crucial for improving fish performance. In this study, we compared the gut microbiota of juvenile black sea bream Acanthopagrus schlegelii among habitats: (1) wild, (2) offshore cage-culture, and (3) pond-culture. We also explored the relationships between the gut microbiota and host-associated environmental factors. Gut samples and associated environmental compartments were investigated using 16S rRNA gene sequencing. Our results revealed significant habitat-specific differences among the gut microbiota of juvenile A. schlegelii. Wild populations of juvenile A. schlegelii had more diverse gut microbiota than populations cultured in pond habitats due to their omnivorous feeding habits and the corresponding abundance of natural food resources. Significant variations in the composition, core taxa, and diversity of the microbiota were also found between the gut and the environmental compartments. However, no significant differences were observed among the microbiota of the environmental compartments in the relatively isolated pond habitat. Source tracking analysis recovered connections between the fish-gut microbiota and the diet, water and sediment environmental compartments. This connection was especially strong between the microbiota of the fish gut and that of the diet in the pond habitat: the diet microbiota accounted for 33.48 ± 0.21% of the gut microbiota. Results suggested that all A. schlegelii shared a core gut microbiota, regardless of differences in diet and habitat. However, environmental factors associated with both diet and habitat contributed to the significant differences between the gut microbiota of fish living in different habitats. To the authors’ knowledge, this study presents the first comparison of gut microbiota among juvenile A. schlegelii with different diets and habitats. These findings enrich our understanding of the gut microbiota of A. schlegelii and help to clarify the interaction between gut microbiota and environmental factors. Our results may also help to guide and improve fish ecological fitness via the regulation of gut microbiota, thereby increasing the efficacy of stock enhancement programs for this species.