Undergraduate University of California, San Diego Ladera Ranch, California, United States
Introduction:: The skin microbiome is a diverse and complex ecosystem whose conditions are constantly changing. Various members of the skin microbial community exhibit co-abundant behavior to perform specific ecological functions in what are referred to as guilds. Such guilds are also dependent on specific niches, or environmental conditions, suited and developed from a specific member. Here we show that the determination of microbial guilds and niches enable targeted modifications of the skin microbiome. We accomplish this by engineering a synthetic community of 9 species of skin bacteria based on their growth rate. After culturing for 5 days under various nutrient-rich conditions, metagenomic and metatranscriptomic sequencing was performed. Initial results demonstrate that the growth conditions changed the growth composition of this assembled skin community. From this, we can further define specific species and conditions which promote or inhibit the growth of selected strains of interest in the community. This, in turn, can aid in determining reliable means to discourage growth of more pathogenic strains in the larger skin microbiome.
Materials and Methods:: A healthy skin microbiome varies between individuals but is dominated by select broad categories of microbes. The engineered synthetic skin microbiome community was based on 9 bacterial strains that are found in the highest frequency across most body sites: Cutibacterium acnes (ATCC KPA17202), Staphylococcus epidermidis (ATCC 12228), Staphylococcus aureus (ATCC SA113), Staphylococcus hominis (ATCC 27844, strain DM 122), Staphylococcus capitis (ATCC 27840, strain LK 499), Staphylococcus warneri (ATCC 27836, strain AW 25), Streptococcus mitis (ATCC 49456, strain NCTC 12261), Corynebacterium afermentans (ATCC 51403, strain CIP 103499 [LCDC 88199]), and Micrococcus luteus (ATCC 4698). OD600 spectromeric measurements were used to characterize growth rates of the strains in isolation in complex Brain Heart Infusion (BHI) media. While the skin is exposed to oxygen, the presence of gradients allows for strict anaerobic bacteria such as C. acnes which was grown anaerobically while the other strains were grown aerobically. All aerobic strains were monitored for 72 hours while C. acnes was monitored for 180 hours. After characterization, the strains were combined into a 1:1 ratio using a Scienion CellenONE liquid printing machine in oxic setting. . A total of 80 nanoliters of each diluted isolate (200 drops of 400 picoliters each) was then added to 200 uL of 1X or 0.1X BHI in a 96-well plate (n = 8 each). Shotgun metagenomic sequencing to assess community diversity and composition after 5 days of growth was conducted.
Results, Conclusions, and Discussions:: The interactions associated with the skin microbiome have broad implications for overall skin health, but it is especially difficult to study this environment effectively to understand and treat applicable skin conditions. In this project, a model synthetic skin community was engineered to optimize composition and diversity in an in vitro system. In diluted BHI, there was less alpha diversity found. However, there was a higher abundance of C. acnes. It was found that C. acnes was able to grow in the synthetic community even in aerobic conditions, and this can be attributed to the presence of oxygen gradients within the system, allowing it to receive nutrients in a more anerobic environment with less oxygen at the bottom of the tested wells. Contrary to previous research findings in the laboratory, it was found that highest alpha-diversity for the community was achieved in undiluted rich growth BHI, and the amount of S. aureus, a key player in the skin microbiome, can be altered from adjusting inoculum proportions. More nutrient rich environments propagate S. aureus growth as well. Given that S. aureus along with S. epidermidis are associated with skin diseases, its presence in rich environments are notable in terms of understanding environments to discourage such ailments
Acknowledgements (Optional): : I would like to thank my Principal Investigator Dr. Karsten Zengler and my graduate student mentor Asama Lekbua for their continued guidance.
