First characterization of the gut microbiome associated with Phascolosoma esculenta collected at a sipunculid farm and from a natural environment in China

Phascolosoma esculenta, a unique economically important aquatic organism in China, has witnessed gradual development in its aquaculture industry for the conservation of wild genetic resources. In this study, we employed high-throughput sequencing of the V3-V4 variable region of the 16S rRNA gene to identify the healthy core gut microbiota and biomarkers in the intestines of wild and cultured P. esculenta. We compared the gut microbiota's structure, diversity, and functional predictions between the two groups to analyze the influence of farming and natural environments on the gut microbiota. The core gut microbiota of both wild and cultured P. esculentamainly belonged to the genus Pseudomonas in the phylum Proteobacteria. Alpha diversity indices, NMDS analysis, and PCoA analysis revealed no significant differences in the gut microbiota between wild and cultured P. esculenta. We observed specific selection of gut microbiota from the phylum Spirochaetes in the intestines of P. esculentaand higher stability of gut microbiota structure in the cultivation group. LeFSe analysis identified differential microbial taxa between the two groups, but due to their relatively low abundance and functional contribution, no significant differences were detected at the level 1 and level 2 KEGG pathways in the predicted functional analysis of the gut microbiota. Linkage analysis of gut microbiota and functional profiles highlighted the significant influence of Pseudomonas, a dominant and core genus, on gut function. Overall, the differences between wild and cultured environments may not significantly impact the core and dominant gut microbiota of P. esculenta, suggesting that it maintains a stable gut environment and basic function through vertical transmission or strong filtering and enrichment of microbial communities in the environment. These findings provide a theoretical basis for the conservation and health assessment of P. esculentapopulations.