This paper describes a dataset of microbial communities from four different sponge species: Ircinia oros (Schmidt, 1864), Ircinia variabilis (Schmidt, 1862), Sarcotragus spinosulus Schmidt, 1862 and Sarcotragus fasciculatus (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.
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