Chiang Mai Journal of Science

     The sea cucumber Holothuria scabra is a commercially valuable species in Asian aquaculture and plays an important role in ecosystem bioturbation. The sustainability of this species has become increasingly important due to the decline of natural populations. Characterizing gut microbial communities under different aquaculture conditions may contribute to improved culture practices for H. scabra. In this pilot-scale study, the intestinal microbiome of adult H. scabra was profiled across three aquaculture environments (concrete tanks, sea pens, and ponds) using high-throughput 16S rRNA gene sequencing. A total of 845 amplicon sequence variants were identified from nine intestinal samples. Bacterial richness and diversity tended to be higher in pond-reared individuals. Principal Coordinates Analysis suggested differences in microbial community composition among the three environments, with Proteobacteria, Firmicutes, and Actinobacteria dominating across all systems. Members of the family Cyanobiaceae (phylum Cyanobacteria) showed relatively higher abundance in pond samples. Functional prediction based on PICRUSt2 indicated environment-associated differences in microbial metabolic potential, with lipid biosynthesis pathways more represented in concrete tanks, carbohydrate and glycogen metabolism more prominent in ponds, and nitrogen-related pathways more represented in sea pen samples. Overall, these results suggest trends in compositional and functional variation of the gut microbiota across aquaculture systems and provide baseline information to support future microbiome-focused investigations in H. scabra aquaculture.