Microbiome-Aware Skincare Through Prebiotic Engineering SECTION 1: ABSTRACT Human skin functions as a vast ecosystem hosting diverse microorganisms that contribute to barrier integrity, immune regulation, and hydration. Disruptions to this microbiome, that can be caused by factors such as harsh surfactants, preservatives, pH imbalance, and environmental stressors, can lead to dysbiosis, a skin condition characterized by increased transepidermal water loss, inflammation, and conditions including acne and atopic dermatitis. New microbiome-friendly cosmetic strategies emphasize restoring microbial balance through prebiotics, probiotics, and postbiotics, yet current skincare approaches remain largely non-personalized and often neglect the important interaction between cosmetic ingredients and the skin’s microbiome. Traditional skincare overlooks the microbiome’s central role in maintaining homeostasis, contributing to a lot of the skin conditions affecting a large proportion of the population.
Microbiome-Aware Skincare Through Prebiotic Engineering
SECTION 1: ABSTRACT
Human skin functions as a vast ecosystem hosting diverse microorganisms that contribute to barrier integrity, immune regulation, and hydration. Disruptions to this microbiome, that can be caused by factors such as harsh surfactants, preservatives, pH imbalance, and environmental stressors, can lead to dysbiosis, a skin condition characterized by increased transepidermal water loss, inflammation, and conditions including acne and atopic dermatitis. New microbiome-friendly cosmetic strategies emphasize restoring microbial balance through prebiotics, probiotics, and postbiotics, yet current skincare approaches remain largely non-personalized and often neglect the important interaction between cosmetic ingredients and the skin’s microbiome. Traditional skincare overlooks the microbiome’s central role in maintaining homeostasis, contributing to a lot of the skin conditions affecting a large proportion of the population.
My final project addresses the need for a more targeted and biologically informed skincare strategy by developing a synthetic biology system capable of producing a skin-relevant prebiotic oligosaccharide in a safe laboratory chassis. The broad objective is to engineer a controllable DNA that synthesizes a prebiotic compound capable of supporting beneficial skin hosts while reducing the biofilm behavior of harmful organisms such as Staphylococcus aureus.
My central hypothesis is that a prebiotic produced by an engineered safe host will shift microbial behavior in a better direction, increasing the growth and persistence of beneficial Staphylococcus epidermidis while reducing S. aureus or biofilm formation. Specific aims include: (1) designing and assembling a DNA encoding the prebiotic biosynthesis pathway; (2) validating production of the prebiotic in a controlled experimental system; (3) testing its biological effects in simplified microbial interaction assays.
Methods will include Benchling-based construct design, DNA synthesis or PCR cloning, Gibson assembly, bacterial transformation, cultivation, and microbiome-relevant growth and biofilm assays. The expected outcome is a validated proof-of-concept platform for microbiome-tuned skincare that shows selective modulation of the microbial ecosystem. This work provides a foundation for future development of personalized microbiome supportive cosmetic strategies and potential expansion into cell-free and consumer friendly applications, contributing to a new line of microbiome-friendly skincare solutions.
Aim 1: Experimental Aim
The first aim for my final project is to design and assemble a genetic circuit in a safe bacterial chassis that produces a prebiotic oligosaccharide by utilizing Benchling for construct design, DNA synthesis or cloning, Gibson assembly, and bacterial transformation. This aim focuses on building the core proof-of-concept system for the project. By constructing a plasmid that can express the biosynthetic pathway under controlled conditions, I can see whether the chosen host can produce the desired prebiotic molecule at a detectable level. This step will also allow me to validate the DNA design, confirm the construct sequence, and demonstrate that the basic engineering strategy is feasible within the scope of the course. Relevant methods include plasmid map design, primer design, sequence verification, and initial expression testing.
Aim 2: Development Aim
The next step following successful completion of Aim 1 is to optimize the pathway for higher prebiotic yield, then test the molecule in co-culture or biofilm assays to determine whether it selectively supports beneficial skin microbes and reduces pathogen-associated behavior. This aim extends the project beyond simple construct creation by asking whether the engineered product has a measurable biological effect. If the first design works, I would improve the system by tuning promoter strength, gene copy number, or expression conditions to increase output and consistency. I would then evaluate the prebiotic in simplified microbiology assays using organisms relevant to skin health, such as S. epidermidis and S. aureus, to determine whether the compound changes growth, adhesion, or biofilm formation in a desirable way. This aim helps connect synthetic biology design to a real functional outcome.
Aim 3: Visionary Aim
The long-term vision of this project is to create a personalized, microbiome-aware skincare platform that can be adapted into a topical product, a cell-free formulation, or a diagnostic-guided cosmetic system for preventing dysbiosis-driven skin disease. In the future, this system could be combined with microbial profiling or skin-sample analysis to help match individuals with formulations tailored to their microbiome state. Such a platform could move skincare away from generic, one-size-fits-all products and toward biologically guided solutions that are more precise and potentially more effective. The broader goal is to support skin health by shaping the microbial ecosystem rather than only treating surface symptoms. If successful, this concept could influence cosmetic development, dermatological care, and personalized skincare products.