Core Bacterial Microbiome in Wild Sea Cucumbers (Apostichopus japonicus) from the Sea of Japan.

Abstract

The taxonomic composition of gut bacterial communities in wild Japanese sea cucumbers, Apostichopus japonicus, from coastal waters of the Russian part of the Sea of Japan was identified by high-throughput sequencing. The bacterial communities were comprised mainly of the phyla Proteobacteria (38.33-57.22%), Actinobacteriota (24.24-29.93%), Firmicutes (12.01-25.12%), and Bacteroidota (1.6-2.17%) that made up a total of 94.5% of the samples studied. As the results showed, the region and habitat have a significant effect on the bacterial structure of the gut microbiome in A. japonicus. The invertebrates from each of the water bodies under study were characterized by their unique sets of symbiotic microorganisms. However, 32 bacterial genera were found in the animals from all of the water bodies. Of these, nine bacterial genera were the dominant taxa in terms of percentage of their representation in the samples: Stappia (15.89-34.68%), Stenotrophomonas (3.45-11.44%), Bacillus (1.05-7.71%), Staphylococcus (4.64-11.76%), Rhodococcus (3.07-11.08%), Corynebacterium (2.55-7.77%), Cutibacterium (15.89-34.68%), Pseudomonas (1.2-1.7%), and Streptococcus (1.09-1.57%). The discovery of bacterial genera common across all samples indicates the existence of a core microbiome potentially essential for the host's health and functions.

Supplementary information: The online version contains supplementary material available at 10.1007/s12088-025-01493-w.