Good Bacteria, Better Skin: The Microbiome Era of Skincare

We tend to focus on the layers of skin, but what sits on top of them is just as important. The skin microbiome, an invisible ecosystem of bacteria, fungi, and other microorganisms, plays a critical role in maintaining balance, resilience, and defense against inflammation. While microorganisms may sound harmful, many of these microbes actually play an essential role in maintaining skin health: they help reinforce the skin barrier, regulate inflammation, and protect against pathogenic invaders by competing for space and nutrients. Each person’s microbiome is unique, shaped by factors such as genetics, environment, skincare habits, and age.

Ahead we'll break down all of your questions about microbiome-friendly skincare, the science behind pre-, pro-, and postbiotics, and whether these ingredients represent a meaningful evolution in skincare or simply the latest wave of marketing-driven innovation.

How does the microbiome affect skin health?

The skin microbiome plays a central role in how skin functions, looks, and responds to stressors. A balanced microbiome helps maintain the integrity of the skin barrier, keeping moisture in and irritants out. It also supports the immune system by signaling when to trigger or calm inflammation, which is key for preventing conditions like acne, eczema, and rosacea. Beneficial microbes further protect the skin by limiting the growth of harmful bacteria. When this balance is disrupted—whether by over-exfoliation, harsh products, or environmental factors—the skin can become more reactive, dehydrated, and prone to breakouts or irritation.

What is the role of bacteria on the skin?

Acting as both protectors and regulators of skin health, bacteria are one of the most influential components of the skin microbiome. Beneficial bacteria help defend against harmful organisms by crowding them out and producing antimicrobial substances. They also contribute to maintaining the skin’s slightly acidic pH, which supports barrier function and discourages pathogenic growth. Beyond protection, certain strains play a role in modulating inflammation and supporting the skin’s immune response. But, not all bacteria are beneficial; when imbalances occur, such as an overgrowth of acne-causing strains, they can contribute to congestion, irritation, and breakouts.

How does the skin barrier function work?

The skin barrier is the outermost layer of the skin and serves as its primary line of defense. It is composed of skin cells held together by lipids, forming a structure often compared to bricks and mortar. This barrier works by sealing in moisture while shielding the skin from environmental aggressors such as pollutants, bacteria, and irritants. It also plays a critical role in preventing excessive water loss, which keeps skin hydrated and supple. When functioning properly, the barrier supports overall skin health. When compromised, it can lead to dryness, sensitivity, and increased vulnerability to irritation.

How do the skin microbiome and skin barrier work together?

The skin barrier and the skin microbiome are closely connected, but they serve distinct roles in maintaining skin health. The skin barrier is a physical structure made up of skin cells and lipids that acts as a protective shield, preventing water loss and blocking external irritants. The microbiome, on the other hand, is the living ecosystem of microorganisms that resides on the surface of that barrier.

While the barrier provides structure and defense, the microbiome supports and regulates it. Beneficial microbes help reinforce barrier function, balance inflammation, and protect against harmful bacteria. When either is compromised, the other is often affected, making their relationship deeply interdependent.

What is dysbiosis in skin?

Dysbiosis refers to an imbalance in the skin microbiome, where beneficial and harmful microorganisms are no longer in equilibrium. This shift can weaken the skin barrier, disrupt its natural defenses, and trigger inflammation. Dysbiosis is often linked to common skin concerns such as acne, eczema, and rosacea. It can be caused by factors like overuse of harsh skincare products, antibiotics, environmental stressors, or lifestyle. When the microbiome is compromised, the skin may appear more reactive, dry, or prone to breakouts.

What are prebiotics vs probiotics vs postbiotics?

Prebiotics, probiotics, and postbiotics are ingredients that support the skin microbiome in different but complementary ways. Prebiotics are compounds that feed beneficial microorganisms already present on the skin, helping them thrive and maintain balance. Probiotics, on the other hand, refer to live microorganisms that, when applied topically, can help reinforce the skin barrier and support a healthy microbial environment. Lastly, postbiotics skincare utilize byproducts created by these microbes, such as enzymes, peptides, and acids, which can directly benefit the skin by calming inflammation, strengthening the barrier, and improving overall resilience. When used together, they can help promote a more balanced, stable complexion.

What ingredients support the skin microbiome?

Ingredients that support the skin microbiome are typically those that nourish beneficial microbes while preserving the integrity of the skin barrier. Prebiotic ingredients such as inulin and alpha-glucan oligosaccharide help feed healthy bacteria, encouraging a balanced ecosystem. A gentle skincare routine with barrier-supporting ingredients like ceramides, fatty acids, and cholesterol also play an important role by reinforcing the skin’s structure to create a stable environment for microbes to thrive. Fermented ingredients and postbiotics can further help by calming inflammation and supporting resilience.

“When it comes to supporting the skin microbiome, I look for products that either help rebalance bacteria or strengthen the skin barrier so that healthy microbes can thrive,” says Dr. Kennedy.

A few formulas Dr. Kennedy recommends include:

• Gladskin Biome Balancing Lotion — “A great option for sensitive or rosacea-prone skin, as it’s designed to calm inflammation while helping restore microbial balance.”
• IMAGE Skincare BIOME+ Dew Bright Serum — “This combines fermented ingredients and barrier-supporting actives to improve radiance while supporting the microbiome.”
• Healing Enzyme Probiotic Face Cream — “A solid choice for acne-prone skin, as it incorporates probiotic ingredients to help maintain balance without clogging pores.”

“Ultimately, the goal is to choose products that work with your skin’s natural ecosystem, not disrupt it," says Dr. Kennedy.

What ingredients damage the skin microbiome?

Certain skincare ingredients can disrupt the balance of the skin microbiome, particularly when used too frequently or in high concentrations. Harsh surfactants, such as sulfates, can strip the skin of its natural oils and disturb both the barrier and the microbes that rely on it. Overuse of strong exfoliants, including high-percentage AHAs, BHAs, and physical scrubs, can further compromise this balance by removing not only dead skin cells but also beneficial microorganisms. Antibacterial ingredients, while useful in specific cases, may also reduce helpful bacteria along with harmful ones. Over time, this disruption can lead to increased sensitivity, dryness, and a weakened skin defense system.

Can microbiome skincare improve acne or rosacea?

Microbiome-focused skincare may help improve conditions like acne and rosacea, particularly by reducing inflammation and supporting the skin barrier. Both concerns are associated with microbial imbalance and heightened immune responses, which can lead to redness, irritation, and breakouts. Ingredients that support a balanced microbiome, such as prebiotics and postbiotics, can help create a more stable environment that is less prone to flare-ups. That said, microbiome skincare is best viewed as supportive rather than curative. While it can complement treatment by calming the skin and improving resilience, more targeted actives are often needed to directly address underlying causes. When used consistently, it can play a valuable role in maintaining clearer, less reactive skin over time.

“When we support the microbiome, we’re essentially helping the skin function the way it’s supposed to—calm, balanced, and better able to defend itself,” says AEDIT Founder and board certified facial plastic and reconstructive surgeon Dr. Kennedy. “That doesn’t replace targeted treatments, but it can make them work more effectively and improve how the skin responds over time.”

Can you repair your skin barrier naturally?

The skin barrier has a natural ability to repair itself, but it needs the right conditions to do so. The most important step is reducing the use of harsh cleansers, over-exfoliation, and strong actives. Instead, opt for products formulated with gentle, hydrating ingredients such as ceramides, glycerin, and fatty acids, which help reinforce the barrier as it recovers. A healthy lifestyle (e.g. staying hydrated, eating balanced and nutritiously, and minimizing environmental stressors) also plays a critical role in overall skill function. The process is not instant, but, with consistency, skin barrier repair is possible.

Does overexfoliation damage the skin barrier?

Yes, over-exfoliation is one of the most common ways the skin barrier becomes compromised. While exfoliation can help remove dead skin cells and improve texture, using exfoliants too frequently or in high concentrations can strip away essential lipids and disrupt the skin’s protective structure. This weakens the barrier and makes it harder for the skin to retain moisture and defend against irritants. As a result, skin may become dry, sensitive, and more prone to redness or breakouts. In many cases, what appears to be acne or irritation is actually a sign of barrier damage.

What is the gut-skin axis?

The gut-skin axis refers to the connection between the digestive system and skin health, mediated by the immune system, hormones, and the microbiome. The gut is home to trillions of microorganisms that help regulate inflammation and nutrient absorption, both of which can directly influence the skin. When the gut microbiome is balanced, it can support clearer, more resilient skin.

Disruptions in gut health (e.g. imbalance, poor diet, or chronic stress) may contribute to inflammation that manifests on the skin as acne, rosacea, or sensitivity. While the relationship is complex and still being studied, it highlights how internal health can play a role in external skin conditions.

Do probiotic skincare products actually work?

Probiotic skincare sits in a gray area between promising science and marketing hype. There is growing evidence that certain probiotic-derived ingredients can support skin health by calming inflammation, strengthening the barrier, and helping maintain microbial balance. Some studies suggest benefits for concerns like acne, eczema, and sensitivity, particularly when it comes to reducing irritation and improving hydration.

However, research is limited, and not all products are created equal. Many formulas do not contain live, stable bacteria, and even when they do, those microbes may not survive long enough on the skin to meaningfully change the microbiome.

In practice, probiotic skincare can be helpful, but it is not essential. Products formulated with prebiotics and postbiotics tend to be more stable and consistently beneficial, making them a more reliable way to support the skin microbiome.

Dr. Kennedy explains, “Your skin isn’t just a surface, it’s a living ecosystem. The microbiome acts as your skin’s first line of defense, helping regulate inflammation, strengthen the barrier, and protect against harmful pathogens. When that balance is disrupted, we start to see issues like sensitivity, acne, and premature aging. Microbiome-friendly skincare is worth it because it works with your skin instead of against it— supporting the good bacteria that keep your complexion healthy, resilient, and better able to repair itself over time.”

Dr. Kennedy’s Favorite Microbiome-Friendly Skincare Picks:

• Gentle, pH-balanced cleansers: Look for sulfate-free formulas that cleanse without stripping beneficial bacteria.
• Prebiotic-rich moisturizers: Ingredients like colloidal oatmeal, honey, and alpha-glucan help feed good bacteria and reinforce the skin barrier.
• Postbiotic serums: These are more stable than probiotics and help calm inflammation while supporting repair.
• Barrier-supporting staples: Products with ceramides, fatty acids, and squalane help maintain the environment where your microbiome thrives.
• Minimalist routines: Over-exfoliating and harsh actives can disrupt microbial balance—simpler routines tend to support long-term skin health.