The diversity, composition, network characteristics and community assembly of intestinal microbiome in sea cucumber reflect the differences in habitats and aquaculture practices

Abstract Background The microbiome of aquatic animals can significantly impact the health and farming success of their hosts. However, the possible differentiation of microbiomes in various aquaculture systems has rarely been studied until now. Here, the microbiomes of five different culture systems for sea cucumber Apostichopus japonicus were compared, including the outdoor pond, indoor workshop, net cage, suspension cage, and marine ranching. Samples of intestinal contents from sea cucumber, surrounding water and sediment were collected from the five culture systems. The microbial diversity, composition, co-occurrence network characteristics, and community assembly were analyzed using 16S rRNA high-throughput sequencing technology. Results Significant differentiations in the microbial diversity, composition, and function were found in various culture systems. Microbial source-tracking analysis indicated that the intestinal microbiomes of sea cucumber were more similar to the sediment than to the surrounding water. Totally, 23 shared core OTUs were identified in the intestinal microbiome of sea cucumber in the five culture systems, belong to the following orders: Rhodobacterales (15), Rhizobiales (3), Flavobacteriales (2), Verrucomicrobiales (1), Campylobacterales (1), and unclassified (1). Meanwhile, unique core OTUs in various systems tended to aggregate toward oligotrophic, potentially beneficial, or pathogenic bacteria. The microbial co-occurrence network characteristics in the marine ranching and suspension cage systems were consistent with those in high-stress habitats, exhibiting lower diversity, complexity, and modularity, and dominated by positive interactions. Conversely, the opposite trends were observed in the indoor workshop, outdoor pond, and net cage systems. Strong diffusion limitations on the intestinal microbial community of sea cucumber, particularly in the marine ranching system, were elucidated. Conclusions The distinct characteristics of the microbiome in various culture systems reflected differences in habitats and aquaculture practices. These findings provide new insights into the impact of aquaculture systems on the microbial community in aquatic animals, and could contribute to healthy aquaculture practices for the sea cucumber industry.