Microbial cultivation approaches to enhance antibiotic discovery

Over the past century of antibiotic discovery and development, the identification of antibacterial small-molecule products of microbial origin following the so-called Waksman Platform has effectively translated into the development of antibiotics. However, in response to the growing threat of antibiotic resistance in bacterial pathogens, there is a pressing need for new antibiotic scaffolds. Taking into account that most microbial species remain uncultured due to our limitations to mimic environmental conditions in the lab, the Waksman Platform is missing a significant number of microbial genomes with potential antibiotic properties. In this sense, the isolation of teixobactin demonstrated that mining of this bacterial dark matter with specialized cultivation devices like the iChip can result in novel antibiotics. The objective of the present work was to study and compare different cultivation approaches and devices used to culture microorganisms from environmental soil samples through 16s rRNA gene sequencing. Out of the studied cultivation approaches (iChip, iPore, iTip, Soil Substrate Membrane System, agar plates, agar spheres, induction of germination, biofilm extraction, non autoclaved agar plates), results showed that the Soil Substrate Membrane System seemed to isolate a higher number of species non isolated by the other techniques. Furthermore, by characterizing the bacterial biodiversity of the bacterial species cultured by each technique, it could be possible to increase the success rate of finding new antibiotic scaffolds through the selection of those cultivation approaches which promoted the growth of specific microbial species or genera