Bioprospecting the Cultivable Bacteria Associated with Trididemnum maragogi from the Saint Peter and Saint Paul’s Archipelago (Brazil) for Bioactive Metabolites

Ascidians and their associated microbiota represent one of the most prolific sources of novel bioactive compounds with application in marine biotechnology. This study investigates the pharmacological potential and metabolic diversity of the bacterial microbiota associated with the ascidian Trididemnum maragogi , collected at Saint Peter and Saint Paul’s Archipelago (SPSPA), Brazil. A total of 45 bacterial strains were taxonomically identified via 16S rRNA gene sequencing into 11 distinct genera, with a predominance of Bacillus and actinomycetes such as Micromonospora , Salinispora , and Streptomyces . Crude organic extracts from bacterial cultures were evaluated for antiproliferative activity against human cancer cell lines (501-Mel and HCT-116). Extracts from Micromonospora spp. (BRB-810, BRB-814, BRB-832) and Salinispora spp. (BRB-803, BRB-808) exhibited potent cytotoxic activity. Metabolomic profiling via HPLC-MS/MS and Feature-Based Molecular Networking (GNPS) enabled the annotation of staurosporines, rifamycins, diketopiperazines, and other bioactive classes, while revealing that approximately 95% of detected features remain unannotated. Furthermore, whole-genome sequencing of Micromonospora aurantiaca BRB-832 unveiled 20 biosynthetic gene clusters (BGCs) related to macrolides, alkylresorcinols, anthracyclines, and novel uncharacterized pathways. These findings highlight T. maragogi and its microbial symbionts as a valuable, underexplored source of novel bioactive natural products with biotechnological potential.