Exploration of the Microbiota Associated with Body Regions Within the Host Sea Cucumber, Holothuria forskali (Echinodermata: Holothuroidea)

The black sea cucumber, Holothuria forskali, is an emerging target species for aquaculture; however, knowledge of its biology remains limited. Investigating its associated microbiota is a crucial step toward developing a controlled and sustainable aquaculture. In this study, the microbiota of three different body compartments of the host H. forskali—namely, the dorsal epidermis, the posterior intestinal content, and the coelomic fluid—were analysed using targeted metagenomics (V3-V4 rRNA 16S Metabarcoding). We compared host-associated communities with bacterial environmental communities across three periods in 2020 at two sites in south Brittany, totalling 309 analyses (36 environmental samples and 273 sea cucumber samples). The objective was to explore the diversity of the sea cucumber microbiota from the external to the internal regions of the animal. Thus, a total of 8695 OTUs were identified and classified into 52 bacterial phyla, 119 classes, and 45,596 orders. The results highlighted (1) anatomical compartmentalisation—with significantly different bacterial assemblages in terms of diversity, composition, and abundance across the three body regions—(2) host versus environment differences, and (3) temporal variations, as microbial community structures shifted significantly in winter compared to summer and autumn. This analysis identified specific taxa and families associated with each compartment with a potential role in host health. Results also showed relationships between the sea cucumber microbiota and their ambient environment. In fact, the presence of common bacterial taxa observed in the sediment and in the gastrointestinal microbiota supported the feeding behaviour of H. forskali. The sea cucumber microbiome thus appears to be compartmentalised “anatomically”, exhibiting a relatively low abundance of bacteria in the coelomic cavity, distinct from that of the microbial communities of seawater and sediments. This study highlighted the importance of the microbiota for the host and confirmed the existence of a core microbiota within H. forskali.