Metagenomic Insights into the Gut Microbial Communities and Functional Dynamics of Bohadschia marmorata in Barobo, Surigao del Sur, Mindanao

Studies on the identification, functional roles, and environmental factors shaping the gut microbiota composition of the sea cucumber Bohadschia marmorata remain scarce. This study aims to (i) characterize the gut bacterial community structure of B. marmorata from Barobo, Surigao del Sur using 16S rRNA gene-based metagenomic analysis, (ii) describe microbial diversity and community composition, and (iii) identify bacterial taxa with potential relevance to probiotic development, opportunistic pathogenicity, and food safety. In November 2024 and February 2025, adult Bohadschia marmorata were collected from seagrass beds in Barobo, Surigao del Sur, with six individuals selected for gut microbiome analysis. The V3–V4 region of the bacterial 16S rRNA gene was sequenced using the Oxford Nanopore MinION platform and analyzed with QIIME2, SILVA, and PICRUSt2. The gut microbiota was dominated by Pseudomonadota (~60%), followed by Bacillota (~25%) and Bacteroidota (~10%). Functional profiling revealed enrichment in energy metabolism, carbohydrate degradation, amino acid metabolism, and oxidative phosphorylation. Several taxa, including Bacillus velezensis, Ruminococcus, and Pseudomonas, showed potential probiotic and biotechnological relevance. These findings provide baseline information for sustainable aquaculture, biomonitoring, and the ecological understanding of B. marmorata.