Investigation of interspecies interactions between marine micromonosporaceae for identification of novel antibiotics

Despite the continued rise in antibiotic-resistant infections, discovery of novel antibiotic scaffolds have been on a steady decline. In part, the decline in new antibiotics can be attributed to the repeated use of relatively standardized methods for natural product isolation, leading to the figurative “low-hanging fruit” being picked. Genomic analyses of actinomycetes have highlighted many biosynthetic gene clusters from which natural products have not yet been isolated under standard laboratory growth conditions. Our study investigated whether interspecies interactions, via co-culture, can stimulate production of novel antibiotics. Marine invertebrate-associated Micromonopsoraceae were used based on the high biosynthetic potential, yet relatively low number of reported chemistry. Microscale (500µL) cultivation followed by bioactivity screening and LCMS-based secondary metabolomics enabled rapid growth and comparative analyses of hundreds of co-culture pairs and monoculture controls simultaneously. Using this approach, we identified a novel antibiotic produced via co-culture of a Micromonospora sp. with a Rhodococcus sp. In addition to progress towards elucidation of the structure, whole genome sequencing of both bacteria was performed to identify the biosynthetic origin and producing organism of the antibiotic. Furthermore, proteins differentially expressed between co- and monocultures were investigated using comparative proteomic analyses. Overall, our study aims to reinvigorate antibiotic discovery by investigating interspecies interactions.