Despite what you’d like to believe, your skin is not sterile. Nor should it be! There’s an entire microscopic world living as part of your skin microbiome.

And that’s a good thing.

So ditch those anti-bacterial soaps and hand sanitizers because, without that skin microbiota, you put your skin at greater risk of developing chronic skin rashes like eczema and psoriasis.

Though we often regard skin as being a barrier to the outside world, research tells us that it’s also home to billions of organisms. And so our skin is much more a living ecology than just layers of cells that you eventually shed.

Hands holding dirt and a sprout

If you worry about what probiotic to take to support your gut microbiome, then your skin microbiome deserves equal respect and care.

Otherwise, you roll the dice as to what organisms will rule your skin’s microbiome… and the results can be frustrating, costly, painful, and embarrassing.

Little care is currently paid to this delicate environment in conventional dermatology which may partly explain why conventional eczema medicines, for example, don’t really work. (And often can make things worse!)

If you’re serious about rebuilding healthier skin, then understanding the microbiota of your skin is paramount!

This is the first of a series of articles examining your skin microbiome and how you can begin restoring normal skin flora again to rebuild healthier skin. The skin microbiome disruption is just one of fifteen underlying root causes of chronic skin problems.


Sleeping newborn baby

What Is Your Skin Microbiome?

Your skin microbiome is a diverse ecosystem where lots of organisms live. And they serve many different purposes, but one key feature is to help your skin stay healthy and maintain a tight barrier from the outside world.

Similarly to your gut, your skin microbiota was colonized at birth. Before that, your skin was sterile within the womb and then exposed to different bacteria depending on whether you were born vaginally or via C-section. (1)

Believe it or not, your skin flora ecology differs depending on where it is located.

There are 3 different location groups are sebaceous (oily), moist, and dry and flat.

For example, the oily regions of the face and the moist regions of the armpits and bottom of your feet differ in the specific flora makeup. It may partially explain why rashes only show up in certain areas (but not everywhere for some people). (2)

No matter where specific skin flora is located, there is a direct line of communication to your immune system. Just as gut flora communicates with your intestinal immune cells, your skin’s immune system is turned on and off thanks to chemical products made by different bacteria living there. (3)

Since one of the key features of chronic skin issues is skin barrier dysfunction, this is important.

Ongoing skin immune activation can spell trouble for rebuilding healthier skin. The problem is only compounded further when you’ve got genetic SNPs present in a key protein called Fillagrin that help maintain appropriate skin barrier function. (4)

Without a healthy skin barrier, you end up with something called “Leaky Skin Syndrome“.

A cousin to Leaky Gut SyndromeLeaky Skin many underlies chronic skin problems like eczema (atopic dermatitis), psoriasis, dermatitis, and other skin rash conditions.


Young hands and elderly hands

What’s A Healthy Skin Microbiota Look Like?

To say that there’s a lot of organisms living on your skin is a bit of an understatement.

In fact, there’s a mix of up to 1 billion organisms per square inch living on your skin. This ecosystem is made up of different types of bacteria, fungi, mites, and viruses that play a role in maintaining a healthy skin barrier. (5)

One reason why skin issues may differ based on your age is that the skin microbiome is in flux throughout your life. The skin microbiome at birth is not the same as in your teenage years. Nor is the teenage skin flora the same as in adulthood. (6)

That’s part of the reason why chronic skin problem treatments must factor in how old you are. What may work for an adult might not be appropriate for a baby.

Generally speaking, there are 19 phyla of bacteria present on the skin with only 3 or 4 predominating. (7)

They include:

  • Actinobacteria (51.8 % of which 22.8 % is Corynebacteria and 23.0 % are Propionibacteria)
  • Firmicutes (24.4 % of which 16.8 % are Staphylococci)
  • Proteobacteria (16.5 %)
  • Bacteroidetes (6.3 %)

And then we have other organisms previously mentioned living in harmony amongst them such as viruses, mites, and fungi. I know the natural inclination is to think this is pretty gross, but they all serve important roles to keep your skin healthy.

However, when your skin is subject to repeated assaults of all kinds, it should be no surprise that skin ecology takes a hit. Insults can include topical antibiotics, harsh body care products, environmental toxins, anti-bacterial soaps, low thyroid levels, and stress.


Colorful bars of soap

Does The pH Balance Of The Skin Microbiome Matter?

It sure does!

Despite the wellness world’s obsession with alkaline foods and diets, your skin should NOT be alkaline.

In fact, the natural (and healthy) pH of skin is between 4.5 to 5. (8)

To put that in perspective, water is typically a pH of 6 to 8.5 whereas soap tends to be a pH of 9-10. Both are more basic (or alkaline) than your skin’s pH and may explain why they both can make your skin worse.

An alkaline environment for your skin’s surface would disrupt the bacteria that live there as well as set your skin up to become friendly to opportunistic organisms.

That said, overly acidic substances would be equally problematic since it is important to keep the skin close to that 4.5 to 5 pH target.

This ideal acidic environment actually prevents “bad” bacteria from growing on your skin. (1) To do this, your skin cells and a healthy skin microbiota work together to make sure that the pH stays where it needs to. (9)

While your skin’s flora is crowding out unfriendly bacteria, fungi, and other opportunistic (and sometimes pathogenic) organisms, it’s also producing antimicrobial peptides, free fatty acids, and pheno-soluble modulins. (9)

Meanwhile, your own cells are busy doing their part to maintain a healthy status quo. Sebocytes make free fatty acids and Keratinocytes make antimicrobial peptides. (9)


Empty desert

The Major Skin Flora Disruptor

The proportions of the above mentioned bacterial phyla are important because when they become unbalanced, you will likely experience skin issues.

As an example, skin flora sampling in those with eczema demonstrates a skin microbiome overloaded with the Firmicutes species. And this imbalance isn’t just present in the areas where you have very apparent rashes. The excess is present even in samples taken from healthy areas of skin. (4)

That’s why you need to take disruptions in this delicate microbiome balance seriously if you want to see a resolution to chronic skin problems.

Increases in certain types of bacteria inherently mean that the overall diversity of your skin drops. These imbalances are seen in conditions such as psoriasis, eczema (atopic dermatitis), and acne. (7)

One specific bacterial player plays a huge role in shifting the tables away from healthy, rash-free skin — Staphylococcus aureus.

In normal, healthy skin, S. aureus is not normally found.

But in cases such as eczema (atopic dermatitis), S. aureus has been found in much larger concentrations in both the persistent rashes as well as the healthy areas of skin.

And they have a distinctive rash that often is mistaken as just a really bad flare — when in actuality, it's a staph infection that requires more attention.


Aside from the problems with the over-sanitization of body care products (like hand sanitizers and anti-bacterial soaps), S. aureus is well-known for its tendency towards developing antibiotic resistance from genes passed to it from other bacteria. (10)

Overgrowth (and infections) of S. aureus are serious requiring medical attention since they can result in MRSA. Since antibiotics are often ineffective, the infected skin and affected tissue must be removed. (11)


Staphylococcus aureus

How Staphylococcus Aureus Manipulates Your Skin Microbiome

One of the biggest reasons that S. aureus is so problematic for the skin microbiome is its ability to use your own skin tissue against you.

Keratinocytes make up the majority of the cells in your outermost layer of skin called the epidermis. (6) By specifically targeting these cells, S. aureus does a tremendous amount of ongoing damage.

One way in which S. aureus does this is by producing chemicals that intentionally stimulate mast cells, trigger inflammatory pathways, and increase the “leakiness” of your skin barrier. It then aggravates keratinocytes by triggering immune responses that ultimately damages these cells. (12)

To be clear, not all forms of Staphylococcus are created equal.

Certain strains actually produce chemicals that inhibit S. aureus as well as their biofilms that help them hide from anti-microbial treatments.

For example, Staphylococcus lugdunensis produces an antibiotic called lugdunin that S. aureus has not been able to develop resistance to. S. epidermidis and S. hominis both create lantibiotics which helped to prevent S. aureus from growing when mixed with certain antimicrobial peptides produced by your own cells. (12)

As a result of ongoing research, there’s a lot more to learn about the missing pieces and underlying triggers that perpetuate chronic skin conditions. And there are new skin microbiome products (like Mother Dirt) available now or coming down the pipeline to help naturally support and rebalance your skin ecology.

CHECK OUT: – Probiotics For Your Skin


1.Grice EA, Segre JA. The skin microbiome. Nature reviews Microbiology. 2011;9(4):244-253. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535073/

2. Grice EA, Segre JA. The skin microbiome. Nature Reviews Microbiology. 2011;9(4):244-253. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535073/figure/F3/?report=objectonly

3. Nakamizo S, Egawa G, et al. Commensal bacteria and cutaneous immunity. Semin Immunopathol. 2015 Jan;37(1):73-80. https://www.ncbi.nlm.nih.gov/pubmed/25326105

4. Lynde CW, Andriessen A, et al. The Skin Microbiome in Atopic Dermatitis and Its Relationship to Emollients. Journal of Cutaneous Medicine and Surgery. 2015:1-8. http://sci-hub.tw/10.1177/1203475415605498

5. Weyrich LS, Dixit S, et al. The skin microbiome: Associations between altered microbial communities and disease. Australasian Journal of Dermatology. 2015 Nov;56(4):268-274. https://onlinelibrary.wiley.com/doi/abs/10.1111/ajd.12253

6. Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nature Reviews Microbiology. 2018 Jan;16:143–155. https://www.nature.com/articles/nrmicro.2017.157

7. Muszer M, et al. Human Microbiome: When a Friend Becomes an Enemy. Arch. Immunol. Ther. Exp. 2014 Dec. http://sci-hub.tw/10.1007/s00005-015-0332-3

8. Lambers H, et al. Natural skin surface pH is on average below 5, which is beneficial for its resident flora. Int J Cosmet Sci. 2006 Oct;28(5):359-70. https://www.ncbi.nlm.nih.gov/pubmed/18489300

9. Chen YE, Tsao H. The skin microbiome: current perspectives and future challenges. J Am Acad Dermatol. 2013 Jul;69(1):143-55. https://www.ncbi.nlm.nih.gov/pubmed/23489584

10. Otto M. Staphylococcus epidermidis – the “accidental” pathogen. Nature Reviews Microbiology. 2009;7(8):555-567. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807625

11. http://www.health.state.mn.us/divs/idepc/diseases/staph/basics.html

12. Geoghegan, Joan A. et al. Staphylococcus aureus and Atopic Dermatitis: A Complex and Evolving Relationship. Trends in Microbiology. 2017 Dec. https://www.cell.com/trends/microbiology/fulltext/S0966-842X(17)30257-3

Jennifer Fugo, MS, CNS

Jennifer Fugo, MS, CNS is an integrative Clinical Nutritionist and the founder of Skinterrupt. She works with women who are fed up with chronic gut and skin rash issues discover the root causes and create a plan to get them back to a fuller, richer life.

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