Sourcing Novel Antibiotics from Soil
By: Joshua Bohm and Sarenna Shaw
Department: Microbiology
Faculty Advisor: Dr. Brinda Govindan
Molecules derived from bacteria have been the major source for antibiotic drugs (2/3 of antibiotics used today originate from soil microbes) that doctors currently prescribe to treat any number of infections. The incidence of antibiotic resistant infections is on the rise, with the possibility that many existing antibiotics will no longer be able to treat common infections in the future. This research project is part of the Tiny Earth Partnership, a global network of student scientists searching for antibiotic producing microbes in soil. We have sampled soil from the Bay Area and several previously untested remote rural areas in Northern California with diverse plant and animal populations. Using our soil samples obtained from various sources, bacteria were isolated and screened for inhibitory activity against safe relatives of ESKAPE pathogens (six nosocomial microbes that exhibit multi-drug resistance and virulence). We discovered several bacterial isolates from these soil samples that showed areas of inhibition when tested against Staphylococcus epidermidis and Staphylococcus aureus. We identified bacterial candidates by PCR amplification of a portion of the bacterial 16S rRNA gene followed by Sanger sequencing. We then performed a chemical extraction on one of the promising microbes (Bacillus aerius) to isolate the compound responsible for its antimicrobial properties. Soil bacteria offer a rich frontier from which to recruit new molecular allies in our continued arms race against pathogen resistance. By harvesting the collaborative power of student scientist research, we hope to advance knowledge of novel antibiotic producing microbes. Directions for future research include further soil analysis, whole genome sequencing to identify novel therapeutic targets and continued chemical extractions to identify antimicrobial compounds.