Characterization of Novel Natural Products Derived from the Skin Microbiome

Emily at lab bench

Students

2020
College

Faculty

Associate Professor of Dermatology

Project Summary

The Grice Laboratory in the Department of Dermatology at the Perelman School of Medicine focuses its research on the study of the skin microbiome and identifying skin microbiota-derived small molecules that mediate cutaneous host-microbe and microbe-microbe interactions within the microbiome. This past summer, I worked with Dr. Lindsay Kalan, a post doctorate in the Grice Laboratory, on an ongoing study to identify and characterize novel natural products produced by the skin microbiome. We hypothesized that the skin microbiome is a rich, yet almost completely unexplored source of small molecules that mediate interactions with the host including cutaneous immune responses and/or exhibit antimicrobial activity against cutaneous pathogens.

We focused on characterizing the natural gene cluster NRPS, or Nonribosomal Peptide Synthetase, because it was highly concentrated in one body site and it was found in 68% of samples. In samples with the cluster, NRPS, the bacteria Corynebacterium amycolatum is dominant. Therefore, we chose to culture strains of C. amycolatum under different conditions to understand in which conditions the NRPS gene is best expressed as well as increase the growth of C. amycolatum while still maintaining NRPS expression.

To accomplish this, we grew C. amycolatum on various types of media plates including brain heart infusion, blood agar, tryptic soy broth, RPMI, and RPMI supplemented with peptone and yeast. We extracted DNA and performed PCR and gel electrophoresis to confirm that the NRPS gene is present in certain strains of C. amycolatum. If so, we extracted RNA and performed RT-PCR to confirm that the NRPS is expressed in the strain. Two strains, LK 10 and LK 19, were confirmed to have the NRPS gene cluster. However, their phenotypes vary drastically as LK 10 sample was derived from a diabetic foot ulcer while LK 19 was derived from the healthy skin of a bellybutton. After determining the best media type C. amycolatum grows best on and has the best NRPS expression, we want to successfully use homologous recombination to create a knockout without the NRPS gene to see if it really is the NRPS gene that is creating the small molecule.

During this summer internship, I gained more experience in basic research and I have learned many useful techniques such as PCR, qPCR, gel electrophoresis, sanger sequencing and DNA/RNA extraction, all of which prove to be integral and valuable in my future in research and medicine. I improved my communication skills by discussing research papers during weekly meetings as well as presented my current week’s progress to the other members of my lab. This internship has given me an immersive experience in the world of research, including listening to multiple thesis defenses and dermatology seminars. I look forward to continuing to work in Dr. Grice’s lab during the academic year.