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Skin Microbiota and Your Health


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Just two decades ago we knew very little about the role of the microbiome in human health. Today, it’s one of the hottest topics in both the scientific literature and the popular media. But while most studies so far have focused on the microbes that live in the gut, researchers are now turning their attention to the skin microbiome—with fascinating results.  

skin microbiota
Skin rashes such as this are often caused by a disruption in the skin microbiota. istock.com/thodonal

Skin is the largest organ of the human body. Healthy, intact skin helps our bodies to retain moisture and provides a protective barrier from physical stress and strain as well as from environmental pathogens.

Skin is composed of the outer epidermis and the inner dermis. Sweat glands and hair follicles with their associated sebaceous glands originate in the dermis and connect to the skin surface through the epidermis. The sebaceous glands form sebum, an odorless oily substance that keeps the skin and hair moist, effectively “waterproofing” it. The amount of sebum produced and retained in the skin varies depending on hormone levels and hygiene habits (1, 2, 3). Sebum also sets up what is known as the “acid mantle,” a protective barrier that places limits on the types of beneficial microbes and pathogens that are permitted to reside in the skin (4).

What role does your skin ecosystem play in your skin and overall health? And how can you actively cultivate a healthy skin microbial community?

Your Skin as an Ecosystem

Human skin hosts a diverse ecosystem of bacteria, fungi, viruses, mites, and archaea (5, 6). It is estimated that our skin harbors approximately 1 billion microbes per square centimeter (7).

Just like any other ecosystem on earth, resident skin ecosystems vary depending on their location on the body and are controlled by moisture and temperature conditions; one’s gender, age, and genetics (8); and individual environmental factors (9, 3).

This skin ecosystem is established at birth, and its development is heavily influenced by the method of delivery. A baby born via the birth canal will be inoculated with Lactobacillus species from mom’s vaginal flora. A baby born via C-section will come into contact with mom’s skin ecosystem first and be seeded with that particular set of microbes (6). From there, the skin microbial community is cultivated by those who care for the infant and altered by routine hygiene practices, personal care products (10), types of clothing that touch the skin (11, 12), exposure to medications (7, 13), time spent in contact with others (14), and time spent in nature (5).

Skin Ecosystem and Disease

Researchers at the forefront of the skin microbiome field are just now beginning to understand how they can shed light on the relationship between microbial communities and disease. This study has been limited by methods of culturing microbes in widely varied “skin climates,” by techniques of genetic analysis, by the challenge of isolating microbes from skin material, and by the fact that current analyses measure the entire historical record of microbes (both living and dead), not just the microbes that may influence health at the present (15, 16, 7).

Nonetheless, new research suggests that there are changes in the skin microbial communities associated with many health conditions, including:

  • acne (17)
  • psoriasis (18)
  • atopic dermatitis, eczema (19)
  • tinea versicolor (20)
  • seborrheic dermatitis (dandruff, cradle cap) (21)
  • rosacea (22, 23)
  • vitiligo (24)
  • warts (25)
  • blepharitis (26)
  • malaria and attractiveness to mosquitoes (27)

What do these associations mean? Does this mean that if you suffer from rosacea you can find relief by changing the microbial community of your skin? This is one avenue of skin microbiome research, but researchers are finding that it’s not easy to draw clear conclusions.

What we do know is that individual members of the skin ecosystem can suddenly change from commensal or beneficial to pathogenic (25, 28, 29, 30, 31). The best example of this is Staphylococcus epidermidis, the cause of staph infections. S. epidermidis is a common and innocuous member of the human skin ecosystem, except of course when it’s not innocuous. S. epidermidis produces different biofilms, has antibiotic resistance, and contains mobile DNA elements when recovered from hospital settings compared to natural human environments. The chimeric nature of some bacteria suggests that their presence or absence is not the primary cause of disease but that there is some environmental trigger controlling pathogenesis (30).

Rosacea has long been treated with antibiotics, suggesting a bacterial root for this common skin condition despite the fact that the mechanism by which bacteria might cause rosacea has not been established. Attempts to better understand the pathogenesis of rosacea have led researchers to investigate the role of the skin mite Demodex (an arachnid) (22). Demodex species inhabit the sebaceous glands of most people, existing on epidermal cells and sebum. People who suffer from rosacea have a higher density of Demodex in their skin, and while this correlation is interesting, it does not explain why rosacea responds to antibiotics. Jarmuda et al. (2012) propose that the bacteria Bacillus oleronius, which have been isolated from Demodex mites from rosacea patients, may be responsible for the rosacea condition.

Why then are some people more prone to higher density of mites? The answer may lie in the composition of skin surface that supports the community. One study demonstrates that the fatty acid composition of skin is significantly different between people with and without rosacea (23). Rosacea patients have reduced levels of long-chain saturated fatty acids, potentially compromising the integrity of the skin barrier. This insight opens the door to rosacea therapies that shift the fatty acid profile of the sebum.

There is a bigger picture unfolding with respect to skin microbial communities and disease, one where the microbes are opportunistic rather than necessarily pathogenic. A recent study suggests that people with immune deficiencies simply have more permissive skin (32) and that skin disorders are associated with compromised immunity.

This study evaluated the skin microbiota of people with rare primary immunodeficiencies (PID) and atopic dermatitis compared to a healthy group. They discovered that the group with PID hosted microbes that were not seen in the healthy controls, including Clostridia species and Serratia marcescens (a common household microbe). The PID group also had less variation between skin ecosystems of the body. In other words, the skin ecosystems of people with decreased immunity are weakened, permitting colonization of opportunistic pathogens.

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Six changes you can make to encourage a healthy skin ecosystem

What Can You Do to Cultivate a Healthy Skin Ecosystem?

While skin microbiome research is in the “wild west” stage today, there are many things that you can do to be proactive about your skin health.

Redefine for yourself what it means to be clean. Soaps, fragrances, and personal care products may alter your skin’s ecosystem in a way that nature hasn’t intended. Wild animals take “dust baths” that effectively bathe their skin in soil bacteria that help to keep them clean. Products that contain preservatives and synthetic ingredients may change the pH of your skin and disrupt your natural ecosystem, particularly if you have decreased immunity.

Consider what touches your skin. While you can’t see it, cosmetics have been found to alter the microbial composition of skin (34). Make-up has also been found to cultivate its own ecosystem with time (35). Get rid of old make-up and consider reducing the role that cosmetics play in your life.

What you put on your skin is critical—but don’t forget what you put in your mouth!

The skin needs over 20 micronutrients to thrive–but most people aren’t getting enough of these essential vitamins and minerals.

The Core Plus bundle from Adapt Naturals was designed to close the modern nutrient gap and provide the nutrients you need for optimal skin (and overall) health.

Consider your clothes. Interestingly, researchers have investigated the microbial growth in synthetic vs. natural clothing. They have found that synthetic materials harbor bacteria that are not native to or are out of balance with the human skin ecosystem, while the microbial communities found in natural fibers mirror the skin microbial communities. Even more, it has been found that washing machines serve to disperse microbial communities among members of a household (12). Most dryers are not hot enough to kill microbes and may even promote growth if clothes are left damp. Air drying clothes in the sun may better disinfect clothing.

Consider your environment. Chronic exposure to sterile or otherwise unnatural indoor environments and the microbes that they support may permit opportunistic species to colonize your skin, particularly if you are already immune compromised. Exposure to natural microbial environments may promote a healthy human microbiome, inside and out (36).

Consider your overall health. While the skin ecosystem is fascinating to study, it does not exist in a vacuum. Addressing only topical and environmental changes to support skin ecology is short-sighted, especially considering the influence of overall immune function on skin permissiveness. Check out my Nutrition for Healthy Skin e-book to better understand the nutrient requirements for optimal skin health, and my Gut Health e-book to learn how to support your immune system.

Reestablish your skin microbiome. Although the research in this area is not yet robust, some evidence suggests that applying ammonia-oxidizing bacteria (AOB) can help to reestablish a healthy skin microbiome. These bacteria have populated our skin microbiome naturally, acting as peacekeepers for the microbial community, but widespread use of soaps, deodorants, and other personal care products wiped them out. Mother Dirt has a line of skin biome-friendly products (such as soaps, shampoos, and sprays) that contain AOB and can be used daily to improve skin health. I and many others in the Paleo community have used these products and found that they can either partially or completely replace conventional soaps and shampoos, with no increase in body odor. You can check them out, and first-time buyers can enter their email address to get 20 percent off plus free shipping.

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Join the conversation

  1. Hello Chris,
    Thank you for this interesting article.
    How about seborrheic keratosis…?
    I’ve got serious problems with them.. it seems they are growing & spreading out all over my body.. if it goes on like this, in 5 years my whole skin is covered with those ugly senile warts and I’m only 42. Already now I’m ashame of my skin and do not like to go swimming in public and try to cover my skin. I’ve been to several skindocs and they all say it’s just about genetics, there’s nothing I can do about it… I can just watch them spreading out. I first notices them after I became mom some 17 years ago, so I suspected it could have some hormonal reason. I also have hashimotos. 10 years ago I had some of them removed by laser, but it hurted like h*ll and they grew back.
    I live in Germany, so many of the recommended US-products are not available here.

  2. Hi Chris,
    I have been suffering from seborrheic dermatitis on my face for several years. For the past 6 weeks under the direction of an acupuncturist, I’ve tried the candida diet (which I believe is similar to Paleo) along with the following supplements: probiotic, garlic, Zymex wafer and gut flora complex (both to promote healthy gut microbiome) with no improvement. Do you have any nutritional or supplement advice, or any recommendations for a practitioner specializing in skin in Los Angeles?

    • Hi Erin,

      I think you’re on the right track trying to replenish your gut microbiome, because many skin ailments have their origin there.

      As a medical skin care specialist, I see a lot of skin problems on people who were born by C-section, due to a disturbed gut flora. I always suggest going to the root of the problem, in addition to trying “external” like creams & lubricants.

      Re. Gut flora: why don’t you try adding Sacchoromyces Boulardii.

      I’ve had very good “skin clearance” results with this probiotic and it easily can be obtained here in the US from the Jarrow co. and also ordered from Swansons. (Take 1 cap twice a day). Good results can often be seen in 1-2 weeks…but that can vary.

      What I also always stress: be sure to add “healthy fats” to your diet…like organic coconut oil, olive oil, ghee, etc. Being so bombarded by the cosmetic industry with advertizing for face/body “creams” as lubricants for the skin, its what we put INTO our body that counts!

      Furthermore, you could also experiment with “fermenting” vegies and fruit yourself. After all, that would yield natural pro-biotics and are even better than those in capsules.

      I’ve done this for many years (ok, I’m from Europe and its a long tradition there, but now live on the East coast) and have (but not always did) extremely good skin!

      Its very easy to do: I cut pieces of organic apples or pears, etc. and put them into a glas jar. I also use frozen Brussle Sprouts or pearl onions (this works and its easy!), Daikon radish and , of course, cabbage, etc. and cover them with brine. (4 C of water and 3 T of fine sea salt makes a Basic Brine. I got this recipe from Dr. David Perlmutter’s Brain book has very detailed instruction for fermenting at home.)

      Let the jar (I cover it with a small shot glas to keep all the apple pieces underwater) sit on the kitchen counter. Depending how warm it is in your environment, the fermentation is often done in a few days. Then tightly close the jar and refrigerate it. This stops the fermentation.

      The fermented apple pieces can then also be made into a terrific “apple sauce” in a blender! Kids love it!

      Good luck to you Erin! I wish you all the best. Experimenting what your body needs and discovering the origin of your ailment is the way to go! Keep reading Chris Kresser’s contributions and his “Gut Health”…and re-read the readers comments here!

    • Erin – Had similar issues, fixed it by removing gluten from my diet (actually I removed all grains from my diet) and went on a high fat low carb diet. You might also need more vit D3 in the form of sunshine. Vit C and grounding will help with the electrical blood flow to your skin. Grounding also may help.

  3. Want to share one more thing the skin microbiota, more properly referred to as the skin flora, are the microorganisms which reside on the skin.
    This article really helps us !
    Thanks For sharing.

  4. Thanks Chris for that informative article. Your points on redefining what it means to be clean is a good point. We use harsh soaps and detergents and after all that even follow up with toners to get that “clean” skin effect. This is definitely not the way we used to cleanse our skin when we were more in tune with nature. We used natural clays that worked with the microbiota on our skin. I also find that products that are pH balanced and natural do wonders with consistent use. I don’t use much makeup anymore (which typically requires those harsh detergents to strip it off) and use clay-based pH-balanced cleanser NuVsio Purifying Mineral Mask to gently remove impurities without stripping the skin of acid mantle or good skin microbes. I also take in clays using CHI Edible Healing Earth for a monthly detox. It worked wonders and now I have a clear glowing complexion!

  5. I have read about a link between digestive problems (low stomach acid) and rosacea. Has anyone else read about this? I had a consultation with an awesome herbalist, and he took one look at me and knew I had digestion problems.

  6. Chris and colleagues, can you offer any insight into the effect the Norwex body cloths may have on the microbiome? Not asking for an endorsement by any means, but there’s a lot of anecdotal evidence of the cloths being used to replace cleansers, with skin clearing outcomes. The cloths are a moderately loose synthetic microfiber washcloth, and the microfibers are manufactured with silver integrated into the fibers.

      • The silver remains within the cloth, as it’s manufactured into the fiber. The silver doesn’t remain in contact with the skin longer than the use time, so I am not sure that its bacteriostatic effect is really in play. I think it’s the light exfoliation and removal of foreign matter but I appreciate all thoughts and comments!

  7. It’s good to see more discussion about the skin microbiome! I run an online support group for natural acne healing and this is an important piece. For a lot of acne, bacteria is a *trigger* (not a cause), which is why antibacterial and antibiotics are used and prescribed but these make the problem worse in the long because by killing off the bad bacteria, they also kill off the good bacteria which is supposed to keep the acne-causing bad bacteria in check!
    A lot of people in my support group have tried antibiotics and had them work temporarily, but then their acne came back several months later, necessitating a higher dose of antibiotics. This is why it’s so important to understand the skin microbiome.
    I have heard from a lot of people that they have also stopped washing their face as vigorously or as much and that that has helped them too.
    If acne is something you deal with, feel free to join the support group for help healing it naturally and identifying the root causes. http://www.facebook.com/groups/acnesupport

  8. This article is very timely for me. I’ve suffered from debilitating hand eczema on and off for the past 5 years. The problem started after I finished a round of antibiotics. Four months ago, I started the Autoimmune Paleo Protocol and began taking Garden of Life Raw probiotics. Within a week, my eczema had cleared up completely. Since I’ve stayed on the probiotic, I’ve added back in every food except grains, dairy and alcohol, and my hands have remained eczema-free. I’m convinced the probiotic has done more than eliminating or adding any other food. I’ve heard a little about the presence of Staph in eczema sufferers but was very curious to know more. Thank you for the report!

  9. Can I just spray some “API Quick Start Aquarium Water Conditioner” on my skin? It looks like it contains similar bacteria. I just can’t justify spending $50 a month on AO+ mist.

    • Are you serious? Ok, we do have evolutionary connections to FISH…but I woud never recommend you do this.
      It might sound harmless: API calls itself “biological” and says it contains “only natural” ingrediences. REALLY! Look at tall the other stuff in it, like preservatives & chemicals to increase its self-life for a year? Fish might not care, but you should!
      The recommended Mother Dirt Products like the “Skin Mist” might be very good – I’ve not tried it, but I trust Chris – its also very expensive and for that reason, I would not buy it! Also, because of its elaborate packaging — so unnecessary and a waste of resources, in this day and age!
      I think for many people the product might represents “a quick fix to great skin” …just as many Diet Products on the market today represent “a shortcut to weight-loss!”
      I maintain: if you restock your GUT with healthy bacterias, it will positively influence your face & body skin! That means, start from WITHIN – I’ve been saying that forever to my clients! – eat healthy fats & foods (no fast-food crap!) and get a very good probiotic! Then load-up on fermented foods…they are very easy to make, but also can be bought.
      AND – not overnight, give it a few weeks – your skin pH will change on your face & body and will become more resistent to “harmful” bacteria….those that can cause skin problems, etc. Your immunity will increased and it fights them. Your body odor will also be greatly reduced and if you feel you do need a deoderant for your armpits – just to make sure – dust them simply with baking soda; its highly basic pH will discourage oder causing bacteria from existing/growing!

      • Well yes, I’m totally serious. The only ingredients I could find in the API product are water, nitrobacter winogradski, and nitrosomonas eutropha (the bacteria found in the Mother Dirt Product). Thank you for your concern.

        • Hey Evan, that’s a very interesting question. I looked it up also and found nothing in the ingredients other than what you listed. Fish are highly sensitive to chemicals (chlorinated water is lethal for them).
          Unfortunately, the Mother Dirt products don’t yet ship internationally so it isn’t an option for me.
          So, thanks for the heads up on the API product, I may test it out 😉

          • After hearing about MotherDirt through a Buzzfeed TestFriends video, I researched AOB and the ingredients in the AO+Mist, and found API Quick Start. I’ve been using 2ml API-QS mixed with water in a 1 liter spray bottle with a mist nozzle. It’s been 3 months since I started, and my skin has become acne-free, less oily, and my overall complexion looks better. The neatest benefit was being able to get rid of my antiperspirant deodorant because I don’t sweat that much, and when I do, it doesn’t have an oder anymore.

            Here’s more info about the API Quick Start and the 2 AOBs in it:


            • Your experience sounds very positive! I also looked in to the data safety info and I’ve been using a solution of the API QS for only a few days so it’s too early to determine any effect as yet. A couple of questions though; how did you arrive at the mix ratio, (my mix is somewhat more concentrated), and are you using water only washing or do you continue to use soaps and shampoos etc. (aside from hand washing, I’ve been soap/shampoo free for over 2 years now). Aside from nurturing my inner micro-biome, I’m particularly interested in the development of a healthy outer micro-biome with respect to improving my immune system.

              • In the beginning, I was worried about the possibility of having a negative reaction, much like the armpit rash the TestFriends girl experienced in that buzzfeed video, so I figured I’d just start with that amount and gradually increase the API-QS if my skin handled it well. The API-QS directions are 10ml for a 38 liter (10gal) aquarium, so I figured 2ml per 1 liter bottle was a safe place to start.

                However, I noticed I hadn’t had much body odor after the first few days, and by the end of the first week, I had no BO at all, so I never added more API-QS because I figured it was already working well at that ratio. I’ve never been a sweaty person, nor have I had much BO, but I was never able to forego deodorant without having a slight musk by the end of the day until I started using the AOB spray.

                There was an awkward drying phase for the first week or so, and I felt like my skin was a little tight at times, but that changed eventually without altering my regimen. My skin kinda normalized moisture on it’s own between the first and second week, and now it has a nice healthy glow. It took slightly over a month for my acne to clear up.

                For washing, I’ve been using the oil cleansing method for about a year with a combination of coconut/olive/castor oil in the shower with warm water.

                • That’s very helpful info. I now feel confident to dilute my spray! In so far as body care products, coconut oil, pure shea butter, and olive squalane oil are what I’ve been using – gotta keep those microbes healthy too.

                  A big thank you for filling me in about your experience.

              • Hi Kitty! Where do you purchase your squalene? Have you been successful with the Mother Dirt spray? Thank you!

                • Hi Amy,
                  I have sourced the squalene oil from several different online outlets; Swansons, iHerb etc. Swansons have a house branded one which I found to be good, and a company called Life Flo Health have one too. I have used the real Mother Dirt spray and found no noticeable improvement over the solution of API. Due to my total avoidance of body/hair detergents for some years now (aside from soap for hand washing) I suspect I have achieved a pretty healthy skin microbiome. My skin has never been healthier.

            • AIBiome’s product is currently under trial for allergic rhinitis, migraines and high blood pressure! Apparently whilst being trialled for acne, participants reported it helping with these other conditions. AOBiome says its product only lasts 1 month out of the fridge. Could you tell me how long the API bottle is supposed to last, and does it say to keep it in the fridge? Also do you need to use filtered water with it? Our tap water tastes of chlorine so we use a filter for drinking water. I’m thinking maybe we should get one for the bath; otherwise every time we bathe we will probably be sterilising our skin again. Rather, it might be better to bathe in API QS.

  10. Chris,
    I am wondering if there is a doctor in the Bay Area that you recommend for young children. I know that Dr. Nett doesn’t take patients under 7, and my three year old with chronic severe eczema needs help.


    • I have had eczema off and on since I was 3 years old. I am now 73. There is a doctor I went to see and he was so helpful in finding out what why my skin was breaking out. He found out what I was bothering my skin by having tests done. Here is his contact info;
      Dr. Timothy J. Smith
      Hope you are able to get help for your child.

      • Elimination diets help but adding in probiotics and prebiotic are essential. Cold water Omegs 3. We use Melaleuca for my granbaby. I am currently researching Chinese Heral cures and Ayruveda fixes. Oh and Melaleuca Renew lotion does wonders. Don’t order from Amazon their way over priced and can be very old. Remove all toxic detergents and cleaning products. If you would like info, please let me know.

    • Add digestive Enzymes and Probiotics to your child’s diet and do an elimination diet of common allergens – gluten, dairy, corn, soy, nuts. I guarantee your little ones eczema will go away when you isolate the problem foods.