Microbial Chemical Diversity and Cytotoxic Potential From Brazilian Ferruginous Caves: A Pioneering Metabolomic Survey

Cave microbiomes represent a rich yet understudied source of chemical diversity with biotechnological properties. Microorganisms in these environments thrive under extreme conditions such as darkness, oligotrophy, and high concentrations of inorganic matter like iron ore. In this study, sediment samples were collected from the aphotic zone of a ferruginous cave in the National Forest of Carajás (Brazilian Amazon). Eight bacterial strains were isolated and taxonomically classified using 16S rRNA gene sequencing, revealing five genera: Serratia, Bacillus, Enterococcus, Aneurinibacillus, and Comamonas. Crude extracts from liquid cultures were analyzed using untargeted LC-MS/MS and processed through feature-based molecular networking on the GNPS platform. The resulting network highlighted the production of structurally similar compound classes across different genera, including cyclopeptides, cholic acid derivatives, and indole alkaloids. Crude extracts were tested for cytotoxicity against HCT-116 and 501mel tumor cell lines, with significant inhibition observed for extracts from Aneurinibacillus, Comamonas, and Enterococcus. Multivariate analysis linked cyclopeptide derivatives to cytotoxic activity. This study offers one of the first insights into the chemical potential of cave-dwelling bacteria in Brazil and underscores their promise for future biotechnological exploration.