Metagenomic insights into the differences in gastrointestinal microbe-mediated metabolism and immunity between wild and captive spotted seals (Phoca largha)

Understanding metabolic and immune functional genes in the gut microbiota of sentinel species, such as spotted seals (Phoca largha), is essential for assessing the health of marine mammals and improving conservation strategies. Information on the gut microbiome is essential for improving conditions in captive species thus aiding in pinniped population restoration, however, it remains poorly understood. In this study, the microbiota in feces from wild and captive P. largha obtained from Liaodong Bay and an aquarium in China were analyzed using metagenomic sequencing. The results showed significant differences in the diversity, composition, and function of gut microbiota between wild and captive P. largha. The bacteria responsible for rapid absorption of energy to product body fat, Firmicutes, were more abundant in the gut microbiota of wild P. largha than in captives. Stronger biosynthesis abilities of nutrients and innate immune factors were observed in the gut microbiota of wild P. largha compared to captive samples. Regarding biomolecules (volatile fatty acids, amino acids vitamins, and several innate immune factors), only the biosynthesis of vitamin B1, secondary bile acids, and a few amino acids were significantly higher in the gut microbiota of the captive P. largha. E. coli, and genera of Bradyrhizobium, Bacteroides, and Rhodanobacter were the dominant biosynthesis functional bacteria in wild P. largha. Overall, these findings showed that wild P. largha had better health status compared to captive species; more importantly, they provide critical data for the development of effective strategies to enhance the growth and health of pinnipeds in captive environments.