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Balance Your Skin’s Microbiome to Clear Acne

Nothing’s more exasperating than conspicuous breakouts. We all get them, and we all spend a lot of effort trying to avoid them. A daily diet of topical antibiotics and antimicrobials prescribed to combat acne may work for a time, but ultimately, they can disrupt the skin’s microbiome balance. It’s now common knowledge that prolonged use of antibiotics kills off beneficial bacteria found in the gut microbiome, tipping the balance in favor of over-colonization by disease-causing pathogens. Similar to the gut’s microbial disruption-disease cycle, skin microbial dysbiosis can lead to skin problems ranging from redness, irritation, rosacea, rashes, eczema, resurgence of acne and adult acne to photosensitization.

Over-production of sebum draws another actor onto the acne stage—the microbe Propionibacterium acnesP. acnes lives in the sebaceous glands and hydrolyses sebum into free fatty acids and propionic acid (hence its name), thus greatly assisting in maintaining proper skin barrier function. A commensal microbe that inhabits all skin, healthy and acneic, alike, it only starts to become problematic when pores become clogged with excess sebum and dead skin cells. To add more complexity to the picture, new research reveals that there are some strains of P. acnes found in acneic skin that are not found in healthy skin, leading scientists to believe that not all species of P. acnescreate acne—just some strains.

Despite our understanding of P. acnes as a commensal bacterium that may or may not become pathogenic depending on the species’ strain, acne sufferers still often reach for the mainstay of popular treatments —benzoyl peroxide—killer of all P. acnes.

Benzoyl Peroxide is the number-one bully of our microbe friends

Benzoyl peroxide (BP) is a powerful antimicrobial that is banned in the European Union in all over-the-counter skin care products. While BP is still approved for use in the U.S., the FDA has issued warnings about it: “The use of certain acne products containing the active ingredients benzoyl peroxide or salicylic acid can cause rare but serious and potentially life-threatening allergic reactions or severe irritation.”

In addition to issuing warnings, the FDA has switched benzoyl peroxide from a Category 1 substance to its current status, Category 3, which means the safety is unknown.

Not only a serious allergy risk for a rare group of people, BP presents other problems for everyone who uses it.

BP accelerates aging:

  • Dries out most skin types and sometimes causes excessive dryness and flaking.
  • Generates free radicals that damage the skin’s structure and cellular DNA.
  • Strong exfoliant properties compromise barrier function, increasing vulnerability to free radical attack from environmental sources.
  • BP-generated free radicals slow the healing process of post-inflammatory hyperpigmentation, prolonging the presence of red and brown marks.

Strong bleaching agent/photosensitizer:

  • Acts as a photosensitizer diminishing sun-protective effects by removing the top layers of skin.
  • Can bleach your eyebrows and hair (it’s peroxide, after all).
  • Can cause increased redness and irritation.
  • BP-generated free radicals slow the healing process. The red and brown marks that are natural to the acne healing process may last weeks longer when BP is part of the daily regimen.

Promotes tumor growth:

  • “Benzoyl peroxide, a widely used free radical-generating compound, promoted both papillomas and carcinomas when it was topically applied to mice.”
  • Skin tumor-promoting activity of benzoyl peroxide, a widely used free radical-generating compound

by TJ Slaga, AJ Klein-Szanto, LL Triplett, LP Yotti, KE Trosko Science 28 August 1981: 1023-1025. [DOI:10.1126/science.6791284]

Some people find that BP works for a time to clear their acne, then simply stops working. Why it stops has not been determined, but my take on it is that repeated applications of a strong antimicrobial may have a similar effect as taking repeated courses of antibiotics. The gut microbiome is disrupted, and the pathogens kept in check by helper microbes begin to take over, resulting in gastrointestinal and bowel disorders of all types. Repeatedly killing off P. acnes, the microbe that helps maintain proper skin barrier function, can result in problems down the road. Most people using BP, regardless of how effectual or problematic it’s been, would welcome a substitute. Fortunately, many natural alternatives do exist.

The Mighty Microbes

Microbial balance in the gut is a new frontier, and skin microbiotic balance is even newer. Scientists are studying how beneficial bacteria applied topically to the skin can work to interfere with the development of acne.

Topical probiotics can benefit the skin in a number of different ways:

  • As a protective shield in a mechanism known as “bacterial interference.”The body’s immune system is distracted by the harmless probiotic bacteria sitting on the skin’s surface, doesn’t invoke an inflammatory response to them, and misses other potential threats that might cause it to react. The result is less inflammation.
  • As an antimicrobial defense.We’ve learned that some microbes have bactericidal properties to aid in limiting pathogens. Probiotics, as well as resident bacteria, can produce antimicrobial peptides that benefit cutaneous immune responses and eliminate pathogens.
  • To have a calming effect.Other types of probiotics send signals to skin cells to arrest attack messages coming from the immune system.
  • To strengthen the skin’s barrier function.Very dry, damaged or acneic skin has reduced numbers of ceramides. In a 2008 study, Dr. L Di Marzio and colleagues, for a limited time period, applied a cream containing the probiotic Streptococcus salivarius ssp.thermophilus (S. thermophilus) to the skin of elderly Caucasian women. In accordance with results of earlier experiments, the skin of the women who received the S. thermophilus cream showed increased skin ceramide level 1 over the control group. Their skin also showed increased hydration.

Daily Regimen for Moderate to Severe Acne


  1. Pantothenic acid: 750 mg and 250 mg l-carnitine, 3x/day
  2. Niacinamide: 500 mg, 1x/day
  3. Probiotics in capsules, powder or in probiotic foods like yoghurt, kimchee or sauerkraut


  1. Cleanse 2x/day with cleansers containing some or all of the following ingredients:
    • Lactic acid—to increase ceramide levels
    • Probiotics—to balance microflora
    • Salicylic acid*—for anti-inflammatory effects (Treatment Cleanser)
    Not recommended: Scrubs contain sharp particles that can cause microscopic tears in the skin and invite invasion from unfriendly microbes like Stapylococcus aureus and Streptococcus pyogenes.

    * Do be aware that the FDA has issued a warning about rare but serious allergic reactions occurring with salicylic acid (as well as benzoyl peroxide). If you develop extreme redness or a rash from an SA or BP product, discontinue use immediately.
  2. Mist 2x/day with green tea (reduces sebum production), probiotics. (Treatment Mist)
  3. Use serums containing vitamin B3 and B5 1x/day, at night. (Treatment Serum)
  4. Follow with an oil blend composed of antioxidants, omega-3 and omega-6 EFAs and tea tree oil. Studies show that tea tree oil helps control P. acnes populations just as well as benzoyl peroxide, but without side effects. (Treatment Oil) 1 or 2x/day, morning and night.
  5. As a final step, you may apply a thin layer of yoghurt containing live strains of lactobacillus and/or bifidobacterium species 1x/day, at night. Stonyfield has an exclusive six live active culture blend of probiotics, which include Streptococcus thermophilus, Lactobacillus bulgaricus, Lactobacillus acidophilus, Bifidus, Lactobacillus casei and Lactobacillus.