Unstable pathogen profile in spotted seal (Phoca largha) gut microbiota and limited turnover with habitat microbiome

It is vital that we monitor the gut microbiota of sentinel species such as spotted seals (Phoca largha) and their association with habitat microbiomes, which can provide critical data for assessing the health of marine mammals and their potential ecological influences. In this study, PacBio technology was used to sequence the full-length bacterial 16S rRNA gene from the feces of captive and wild spotted seals, as well as samples from a wild population and their habitats. Based on the pathogen identification results, the gut microbiota of wild and captive spotted seals showed similar levels of pathogen richness and abundance. In particular, the pathogen profiles in wild spotted seals were more variable, with a high risk of disease in a minority of individuals. Meanwhile, the gut microbiota of spotted seals was significantly less diverse than their habitat microbiomes. Firmicutes and Proteobacteria dominated the gut microbiota of spotted seals and their habitat microbiomes, respectively. Furthermore, network analysis revealed that the gut microbiota of spotted seals was simple and weak. The ratios of microbial turnover between spotted seal gut microbiota and their habitat microbiomes were further analyzed using SourceTracker, and the estimated values were low (< 0.1%). These results provide baseline data on pathogen profiles in spotted seals and their potential interactions with habitat microbiomes.