Microbiome in marine sponges have been recognized as important sources of many natural products with potent biological activities. These bioactive natural products play an ecological role as chemical defense to protect sponge hosts from predators and microbial infections. From biotechnological point of view, they have become an interesting target in recent years for being developed towards clinically used medicines, such as anticancer, antiviral, and antimicrobial drugs [1]. However, the inherent difficulty in cultivating the majority of sponge-associated microbiome under normal laboratory conditions has hampered attempts to study their diversity and pharmacological potential [1]. In this present study, we applied a cultivation-independent approach by metagenomic 16S illumina MiSeq sequencing technology to investigate the genetic diversity of symbiotic microbiome associated with five species of Indonesia marine sponges (Rhabdastrella sp., Theonella sp., Aaptos sp., Calyspongia sp., and Petrosia sp.) in comparison with that of planktonic microbes present in the seawaters surrounding the sponge’s habitat. We particularly compared the microbial composition of two Theonella sp. specimens living in geographically different locations (Kapoposang Island and Buton Island). The 16S-cloning approach indicated that Kapoposang Rhabdastrella sp. harbored “Candidatus Entotheonella” [2], as-yet uncultivable bacteria genus known as the producers of numerous polyketides and modified peptides previously reported from the Japanese sponges Theonella sp. [3–6]. We subsequently detected modular polyketide biosynthetic machinery called polyketide synthase (PKS) in sponge's microbiomes through the illumina sequencing of DNA regions encoding ketosynthase (KS) domain, a key component in PKS. Interestingly, diverse ketosynthase (KS) sequences were encoded on the microbial metagenome of Kapoposang Rhabdastrella sp., which showed similarity with those from type I PKS of known compounds. This suggests the potency of the symbiotic microbiome in Kapoposang Rhabdastrella sp. as a source of pharmacologically relevant polyketides.
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