The bacterial community is an essential component of the aquaculture pond ecosystem, which not only improves and restores the aquaculture environment but also maintains a stable ecological equilibrium with the external environment. Here, Illumina 16S rRNA sequencing was conducted to characterize the bacterial community in the ecosystem of sea cucumber Apostichopus japonicus culture ponds, as well as their correlation with overall community structures. The alpha-diversities of bacterial community among water, sediment, and the gut of A. japonicus were consistent across culture ponds from different areas. Specifically, the richness and diversity of bacterial communities were the highest in sediment, followed by the gut, and the lowest in water. The dominant bacterial community among multiple media was Proteobacteria, which occupies a large proportion of the bacterial community structure, followed by Bacteroidetes and Verrucomicrobia. Highly similar bacterial community structures were present in multiple media among different areas, which provides evidence for deterministic natural evolution. Meanwhile, there was a significant difference (p < 0.05) in the specific bacterial communities across the multiple media. The specific functions of the multiple media in the ecosystem are the main reason for the formation of different bacterial communities. This work demonstrates that bacterial communities are the result of natural evolution within the ecosystem during adaptation to the required environment.

Background Gut microbiome and their metabolites are increasingly recognized for their pivotal role in regulating the health and growth of the host. The mechanism by which the host-gut microbiome co-metabolism affects the growth rate of sea cucumber (Apostichopus japonicus) remains unclear. In this study, the intestinal wall tissues of fast-growing (FG) and slow-growing (SG)A. japonicuswere collected from the full-sib family for 16S amplicon sequencing, metagenomics, metabolomics, and transcriptomics analyses. Results The results showed a marked variation in the gut bacterial community ofA. japonicuswith different growth rates. Compared with SG group, FGA. japonicushad a higher abundance of Bacteroidetes. Many of these bacteria were associated with the degradation of polysaccharides, which could potentially affect growth performance. The abundance of Proteobacteria, however, was found to be higher in SGA. japonicus, thereby increasing the potential risk of disease. The metabolome results were further supported by the predicated KEGG functions of the gut microbiomes, lots of metabolites related to the metabolism and biosynthesis of fructose 6-phosphate, arachidonic acid, oleic acid, and dihydroxyacetone phosphate were upregulated in the FGA. japonicus. Furthermore, the genes (IGF1,HK,PK,PCK1) were significantly upregulated in the FGA. japonicus, which were mainly enriched in the metabolic pathways of lipids, amino acids, and carbohydrates. Conclusions Gut bacterial community via their unique metabolic pathways, which in turn affected the metabolic phenotypes of the organism and eventually led to differences in growth performance ofA. japonicus. These findings might help understand the molecular mechanisms of growth gap in sea cucumber, thereby increasing the mariculture production.