Genomic and Metabolomic Insights into Metabolites of a Streptomyces Isolate Associated with Chromodoris quadricolor, a Red Sea Nudibranch

The marine invertebrate-associated microbiome has garnered significant interest in recent years due to its wealth of novel genes that can be explored for biomining. By combining genomics with untargeted data-dependent mass spectrometry (MS) and molecular networking, we characterized the secreted metabolome of <i>Streptomyces</i> sp. In a previous study, we isolated and characterized a strain of <i>Streptomyces</i>, designated as strain 34, from the nudibranch <i>Chromodoris quadricolor</i>, collected by SCUBA diving in the Red Sea near El Tor in the Gulf of Suez, Egypt. In the present study, the <i>Streptomyces</i> isolate was identified as <i>Streptomyces tunisiensis</i> GCF 039538125 1 (<i>p</i>-value: 0). Genomic and metabolomic analysis reveal 36 predicted biosynthetic gene clusters. A total of 569 metabolites were detected in the culture, with 86 of these being identified based on standards and public spectral libraries. Moreover, a single lassopeptide synthesis gene cluster was found in both the genome and the metabolic extract, along with various sets of siderophores identified in the metabolic extract. Since the metabolic processes of marine invertebrate microbiomes are poorly understood, our findings are a significant addition to the research on metabolism in host microbiomes.