Comparative Analysis of Gut Microbial Community Structure of Three Tropical Sea Cucumber Species

Based on 16S rRNA gene high-throughput sequencing technology, the microbial community structure in the gut of three tropical sea cucumber species, Holothuria atra, Stichopus chloronotus, and S. monotuberculatus, and their habitat sediments were analyzed. The OTUs in the gut contents of S. monotuberculatus, S. chloronotus, H. atra, and their sediments were 2489 ± 447, 1912 ± 235, 1628 ± 150, and 4162 ± 94, respectively. According to alpha diversity analysis (Ace, Chao1, Shannon, Simpson), the richness and diversity of microflora in the gut of all three sea cucumber species were significantly lower than that in sediments (p < 0.01). Anosim analysis showed that the intra-group differences were less than the inter-group differences (R > 0), and the microbial community composition of the sediment was distinctly different from those of three sea cucumber species (p < 0.05). UPGMA tree and Anosim analysis also revealed that the gut microbial communities of H. atra and S. chloronotus were more similar than that of S. monotuberculatus. Proteobacteria was the predominant phylum in all samples, and there was no significant difference in relative abundance among all groups. Actinobacteria was also a dominant phylum, and the relative abundance in S. chloronotus was significantly higher than that in other samples (p < 0.05). Potential probiotics and sequences related to Lactobacillus and Pseudomonas that may be developed for sea cucumber culture were also found in the study. It is speculated that the main reason for the difference in microbial communities between gut microbiota and environmental sediments may be the unique and quite different environment in the digestive tract of sea cucumbers. Whereas, the differences in gut microbiota among the three sea cucumber species were caused by selective feeding. These findings may provide basic data for tropical sea cucumber gut microflora studies and assist in the sea ranching and aquaculture development of the tropical sea cucumber species.