Jellyfish, microorganisms, and the marine environment collectively shape a complex ecosystem. This study aimed to analyze the microbial communities associated with five jellyfish species, exploring their composition, diversity, and relationships. Microbial diversity among the species was assessed using 16S rRNA gene sequencing and QIIME analysis. Significant differences in bacterial composition were found, with distinct dominant taxa in each species: Mycoplasmataceae (99.21%) in Aurelia coerulea , Sphingomonadaceae (22.81%) in Cassiopea andromeda , Alphaproteobacteria _unclassified (family level) (64.09%) in Chrysaora quinquecirrha , Parcubacteria _unclassified (family level) (93.11%) in Phacellophora camtschatica , and Chlamydiaceae (35.05%) and Alphaproteobacteria _unclassified (family level) (38.73%) in Rhopilema esculentum . C. andromeda showed the highest diversity, while A. coerulea exhibited the lowest. Correlations among dominant genera varied, including a positive correlation between Parcubacteria _unclassified (genus level) and Chlamydiaceae_ unclassified (genus level). Genes were enriched in metabolic pathways and ABC transporters. The most abundant potential pathogens at the phylum level were Proteobacteria, Tenericutes, Chlamydiae, and Epsilonbacteraeota. The differing microbial compositions are likely influenced by species and their habitats. Interactions between jellyfish and microorganisms, as well as among microorganisms, showed interdependency or antagonism. Most microbial gene functions focused on metabolic pathways, warranting further study on the relationship between pathogenic bacteria and these pathways.
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