Metagenomic characterization of the gut microbiota of Actinopyga echinites reveals ecological functions and untapped biotechnological potential

Abstract Host-associated microbiomes are increasingly recognized as key drivers of ecosystem functioning, yet the microbial diversity of tropical sea cucumbers remains poorly understood. This study provides the first metagenomic characterization of the gut microbiota of the vulnerable (IUCN Red List) sea cucumber, Actinopyga echinites , from the Philippines, and explores its ecological and biotechnological significance. Gut samples collected from Barobo, Surigao del Sur, were analyzed using Oxford Nanopore 16S rRNA sequencing and bioinformatic profiling. The gut microbiome was dominated by Bacillota and Pseudomonadota , with Clostridia , Bacilli , and Gammaproteobacteria representing the major taxonomic groups. Diversity analyses revealed a moderately diverse but highly even microbial community (Shannon index = 2.45; Pielou’s evenness = 0.95), indicating a stable and functionally balanced gut ecosystem. Core microbial taxa included Morganella morganii and Bacillus spp ., while several environmentally derived taxa reflected continuous recruitment from sediment-associated habitats. Functional prediction analyses suggested strong capacities for carbohydrate degradation, protein turnover, nutrient remineralization, and anaerobic fermentation, highlighting the microbiome’s contribution to host nutrition and benthic nutrient cycling. Notably, several bacterial taxa were associated with the production of hydrolytic enzymes, antimicrobial peptides, and biosurfactants with potential applications in aquaculture, biotechnology, pharmaceuticals, and environmental bioremediation. The coexistence of fermentative, probiotic, and metabolically versatile microorganisms suggests that the gut of A. echinites functions as a microbial bioreactor linking host physiology to ecosystem processes. These findings establish a critical baseline for understanding host–microbe interactions in tropical holothurians and identify A. echinites as a promising reservoir of microbial resources for sustainable conservation initiatives and marine biotechnology.