Everything You Need to Know About the Skin Microbiome

While researchers are still studying the skin microbiome to learn more about it, here's an overview of what they know, how it affects your skin, and how to keep it balanced for a healthy complexion.

“Just like your gut, your skin has its own microbiome, a diverse community of microorganisms that live on its surface,” says Trevor Cates, ND, a board-certified naturopathic doctor and the founder of the Spa Dr. skin-care and wellness line, who’s based in Park City, Utah. “This includes not only bacteria, but also fungi, viruses, and mites that help protect your skin barrier, maintain hydration, and even influence inflammation.”

“When this delicate balance is disrupted, it can lead to common skin issues like acne, eczema, rosacea, and even premature aging,” Dr. Cates says. “Supporting your skin microbiome is one of the most important, and often overlooked, steps to achieving healthy, radiant skin.”

“A healthy microbiome regulates inflammation, protects against harmful microbes, and supports the repair process when the skin is damaged,” says Chloë Ward, a Santa Barbara–based functional diagnostic nutrition practitioner and certified integrative nutrition health coach who specializes in acne and inflammatory skin conditions. “Together, the microbiome and skin barrier maintain the integrity and resilience of the skin.”

Other key benefits of a well-balanced skin microbiome include:

• Acne Prevention A balanced microbiome helps keep acne-causing bacteria, such as Cutibacterium acnes (formerly Propionibacterium), from overgrowing and triggering breakouts.

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• Reduced Risk of Eczema Flares People with atopic dermatitis (eczema) often have higher levels of Staphylococcus aureus bacteria, which can worsen symptoms. A healthy microbiome helps keep these bacteria in check, which may reduce the frequency and severity of flares.

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• Potential Psoriasis Relief Psoriasis is a complex autoimmune disease, but research shows a clear link between its symptoms and an imbalanced microbiome. Specifically, psoriatic lesions often show a decrease in beneficial bacteria and an increase in inflammatory ones like Streptococcus.

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• Reduced Severity of Vitiligo Newer research suggests that people with vitiligo have a different microbial composition on their skin than those without the condition. This may one day lead to new treatment strategies that focus on microbiome balance.

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• Help in Managing UV Exposure A healthy microbiome regulates the skin’s immune response after sun exposure by breaking down specific compounds that UV rays create on the skin.

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“The gut-brain-skin axis has long been around for several decades,” says Kseniya Kobets, MD, the director of cosmetic dermatology at Montefiore Einstein Advanced Care in Elmsford, New York. Gut health can affect stress and hormone levels, which in turn affect the skin, she says.

“If your gut is inflamed or compromised because of dysbiosis (an imbalance of gut bacteria), parasites, pathogens, or low stomach acid, your body may not be able to properly absorb key nutrients, no matter how clean your diet is,” says Ward.

Your skin microbiome is relatively resilient, but certain skin care products, environmental factors, and lifestyle choices can disrupt its delicate balance.

Here are some of the biggest culprits, according to experts:

• Overcleansing and Harsh Soaps Washing your face too often or using the wrong products is a common skin care mistake that can strip your skin of its natural oils. “Overcleansing is a big one — especially with harsh soaps, alcohol-based toners, or aggressive exfoliants,” says Hannah Kopelman, DO, a New York City–based cofounder of DermOnDemand, a national dermatology telemedicine provider.
• Using Too Many Active Ingredients It’s best to stick to a simple skin-care routine and avoid irritating ingredients. Dr. Kopelman cautions against layering strong retinoids, acids, and benzoyl peroxide. “Antibacterial washes and wipes, especially when used frequently, can also be damaging,” she says.
• Not Washing Your Skin Care Tools Just as your skin hosts its own ecosystem of microbes, so do your towels and beauty tools. “Not washing towels, makeup brushes, and not washing the face after sweating can all promote imbalance or overgrowth of bacteria or yeast on the face,” says Dr. Kobets.
• An Unbalanced Diet What you eat impacts your gut health, which is directly linked to your skin via the gut-skin axis. A diet high in ultra-processed foods and sugar can promote inflammation that shows up on your skin.

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• Taking Certain Medications While often necessary, oral antibiotics don't know the difference between “good” and “bad” bacteria. They can wipe out beneficial microbes on your skin and potentially alter the long-term composition of your microbiome.

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The best way to support your skin’s microbiome is to protect it from damage by starting with a “less is more” approach that focuses on gentle, consistent care rather than an overly complex routine.

“Using lower pH cleansers that are closer to physiologic pH (in the 4.5 to 5.5 range) will help maintain a proper skin microbiome,” says Kobets.

“Following a well-balanced diet rich in fiber, prebiotic foods (like onions, garlic, and leeks), and for some, probiotic-rich foods (like sauerkraut or kefir), helps nourish your gut microbiota, which in turn supports healthy skin,” says Cates.

Topical probiotics, though, can also do more harm than good, says Ben Johnson, MD, the founder of Osmosis Beauty, who’s based in Evergreen, Colorado. “The secret to having a good microbiome is having an intact barrier with all the lipids present for the bacteria to feed on,” he says. “This means avoiding harsh acids, Retin-A, daily exfoliation, and aggressive cleansers.”

“The science is still evolving, and we don’t yet have a gold standard for interpreting results or knowing what to do with the data,” says Kopelman. “I wouldn’t discourage someone from trying it if they’re curious, but I’d caution them not to overhaul their skin care routine based on a single test. Until we have more robust, clinically validated guidelines, these kits are best seen as exploratory tools — not diagnostic ones.”

If you’re really interested in testing, Cates recommends focusing on gut microbiome testing, which currently provides more actionable insights for skin health, especially if you're working with a naturopathic physician or functional medicine doctor.

• A balanced skin microbiome, the community of microorganisms living on your skin, is essential for maintaining a healthy skin barrier and managing inflammatory conditions like acne, eczema, and psoriasis.
• You can support your skin's ecosystem by protecting it from damage; this includes using gentle, low-pH cleansers and avoiding overly complex routines with too many harsh, active ingredients.
• Because of the gut-skin axis, supporting your gut health through a well-balanced diet rich in fiber and whole foods can directly and positively influence the health of your skin.
• While at-home microbiome testing kits are available, they currently lack the clinical validation needed to guide health decisions, so it's always best to consult a board-certified dermatologist with any skin concerns.