Eczema & The Microbiome

The microbiome plays a crucial role in mitigating eczema by regulating the immune system, generating protective skin compounds, and warding off pathogens.

Understanding the relationship between the skin microbiome and eczema is key to effective eczema treatment.

The microbiome has increasingly been recognized as a pivotal player in mitigating eczema flares and, importantly, expediting their resolution. Neutral or beneficial microorganisms, often referred to as "commensals" or “mutualists”, contribute to skin health through immune system regulation, the generation of compounds that can safeguard the skin, and warding off pathogenic microorganisms.

In this blog post, we delve into the intricate relationship between the microbiome and eczema, explore the factors that influence which microbes are found on the skin, and offer practical advice for preserving a healthy microbial community in ways that help to manage eczema symptoms.

How A Healthy Microbiome Controls Eczema

The term "microbiome" often refers to the complex community of microorganisms, including bacteria, fungi, viruses, and other microscopic life forms, that inhabit our bodies.(COS 2009) These skin microbes reside on the skin barrier and extend into the skin's dermis.(SEN 2016)

The specific composition of the skin microbiome varies among individuals, but some of the most prevalent bacterial groups found on healthy skin include Staphylococcus epidermidis, Propionibacterium acnes, and Corynebacterium.(Byrd et al., 2018)

The key functions of a healthy skin microbiome include:

  • Infection protection (Colonization resistance): A healthy skin microbiome can prevent the colonization and overgrowth of harmful pathogens by competing for space and nutrients, as well as by producing antimicrobial compounds, such as bacteriocins. These molecules are capable of selectively inhibiting the growth of harmful bacteria while preserving beneficial bacteria (Nakatsuji et al., 2017)
  • Skin barrier strength: The skin microbiome plays an essential role in maintaining the skin's barrier function. Microorganisms on the skin produce enzymes that help break down sebum and other substances, which in turn contribute to the formation of the acid mantle, a thin acidic film on the skin's surface. This acidic environment is critical for the integrity and function of the skin barrier, as it helps keep the skin moisturized and protects it from external irritants and allergens.(Mukherjee et al., 2018)
  • Modulation of immune responses: A healthy skin microbiome maintains a delicate balance between promoting immune tolerance and eliciting an immune response to protect the skin from pathogens. Commensal bacteria interact with immune cells, such as Langerhans cells and T cells, to regulate the release of various cytokines and other immune mediators. This interaction is crucial for maintaining a controlled and balanced immune response, preventing excessive inflammation that could damage the skin and contribute to various skin disorders, including eczema.(Naik et al., 2015)(Nature)
  • Promotion of skin health (homeostasis): A healthy skin microbiome helps maintain skin homeostasis, the balance between the skin's cellular processes, such as cell proliferation, differentiation, and apoptosis (i.e., death of damaged cells). Microbial metabolites and other signaling molecules produced by commensal microorganisms can influence the response of skin cells, promoting skin renewal and repair. This helps maintain the skin's structural integrity and its ability to function as a protective barrier.(Dreno et al., 2016)
  • Wound healing: The skin microbiome is involved in the complex process of wound healing, which includes inflammation, proliferation, and remodeling phases. Commensal microorganisms can produce growth factors, stimulate angiogenesis, modulate immune responses, and even help degrade the extracellular matrix to facilitate the migration and proliferation of skin cells. A healthy skin microbiome has been shown to promote effective wound healing and prevent complications such as infections and chronic wounds.(Grice & Segre, 2011)

The astute reader will see the list above and recognize that all five of these functions provide critical support in the prevention and resolution of eczema flares.(Belkaid & Segre 2014)(Grice & Segre 2011)

Research has shown that individuals with eczema often have a disrupted skin microbiome, with a reduced diversity of microorganisms and elevated levels of specific bacteria that are enriched with inflammation, such as Staphylococcus aureus.(Kong et al., 2012)(Byrd et al., 2018)

What Causes Changes in the Microbiome?

Various factors can induce changes in the skin microbiome, such as age, diet, medication, and environmental factors.(DIM 2019) Daily interactions with our surroundings, including contact with other people or objects, can introduce new microorganisms to our skin and change its overall composition in the short term.(ROS 2017) Sweat, diet, and exposure to chemicals can all influence the skin's microbial balance.(BYR 2018)

However, the microbiome and the body are generally self-regulating. They strive to return to a state of homeostasis with their long-term environment.

Persistent dysbiotic microbiome composition is primarily driven by three factors:

  • A disrupted skin barrier (including a lack of long chain ceramides and disorganization in the skin barrier)

  • Sustained exposure to environmental factors (such as a new roommate or a move to a new location)

  • The use of skin care products

In the following sections, we will delve deeper into these factors and their impact on the skin microbiome.

Skin Barrier and Microbiome Composition

A weakened skin barrier can result in higher levels of inflammation. In turn, this can alter the skin’s surface environment in ways that allow for specific microbes to thrive. 

Many people with eczema have a root-cause problem with skin barrier formation that decreases skin barrier strength. In these patients, their skin (even in locations on the body where there is not an eczema flare) will show elevated levels of S. aureus relative to that of an individual without eczema.(Irvine et al., 2011) 

Though S. aureus is a common resident of the skin microbiome, certain strains of this bacteria can become pathogenic if induced to do so, particularly in individuals with a compromised immune system.

Environment and Microbiome Composition

Environmental factors play a significant role in shaping the composition of the skin microbiome. Exposure to toxins, pollution, and other harsh environmental elements can lead to an imbalance in the skin microbiome, favoring the growth of potential pathogens.(Fyhrquist et al., 2014) 

In addition, gene transfer and expression in microorganisms can occur in response to environmental stressors, contributing to dysbiosis and potentially exacerbating eczema symptoms.(Shade & Handelsman, 2012)(ZEL 2023)(ARC 2010)

Skin Care Products and Microbiome Composition

The ingredients in skin care products can influence which microbes are found on the skin. For example, the use of harsh soaps or over-cleansing can strip the skin of its natural oils and decrease the diversity of microbes, potentially exacerbating eczema symptoms.(Skroza et al., 2018) 

Some skin care ingredients are even intentionally designed to induce inflammation in an effort to reduce fine lines and wrinkles, and other beauty concerns. As discussed above, inflammation can then promote the growth of unfavorable, or even pathogenic, microbes. Some common skin care ingredients are toxic to the microbiome, driving a shift to more pathogenic microorganisms. 

Further, there are treatments for eczema, like bleach baths, that are unintentionally resulting in an unhealthy balance in your skin community. 

Nurturing Your Skin Microbiome for Eczema Management

Maintaining a healthy skin microbiome is crucial for the effective management of eczema-related symptoms. However, it's important to approach microbiome maintenance with caution. While an unbalanced microbiome might not be optimal for controlling inflammation, healing the skin, and reducing the effect of environmental triggers, it is still preferable to an infection.

Understanding “Unbalanced” Versus Infection: When Should You Be Concerned?

Understanding the distinctions between a dysbiosis of the microbiome and an infection is crucial to understand the role that each plays in eczema.

One example comes from that of S. aureus. S. aureus is broadly considered a common skin commensal and normal member of the skin microbiome. In eczema sufferers, however, the disrupted skin barrier feeds S. aureus which can lead to a dysbiotic microbiome, which in turn can no longer regulate the immune system or repair the skin barrier, resulting in a sustained flare. 

This imbalance of S. aureus would be considered “unbalanced”, and like a canary in the coal mine, can be used as both a marker of skin barrier strength and the severity of an eczema flare.(KOH 2022)(FOL 2022) On the other hand, an infection occurs when “pathogenic” microorganisms (whether they be bacteria, viruses, or fungi) invade the body's tissues causing damage to cells and eliciting an immune response. In the context of skin infections, this typically involves redness, swelling, warmth, and sometimes pus production. 

Infections are different from the elevated levels of S. aureus that can occur during a flare. Infections involve active invasion of the pathogens, potentially leading to significant tissue damage and a more severe immune response. See our section on infections to learn more and consult your physician to determine if you have an infection.

The Risks to the Microbiome of Treating an Infection When None Exists

Always follow your doctor’s direction. We offer the below only to add context to treatment decisions and anticipated outcomes. 

The use of antibiotics, bleach baths, and other disinfection methods can have both positive and negative effects on the skin microbiome. Although these methods can help to control infections and/or reduce the bacterial load in certain skin conditions, they can also lead to dysbiotic microbiome and an increased risk of infection when used excessively or inappropriately. Additionally, their use could result in long-term skin conditions such as eczema or dermatitis.(Kong et al., 2012) 

For example, systemic antibiotics may be necessary to successfully treat an infection, but there is poor evidence that the use of systemic antibiotics to reduce S. aureus in noninfected individuals will improve eczema-related symptoms.(BAT 2010)

A decrease in microbial diversity created by the use of antimicrobials or chemicals (e.g., bleach) could provide an opportunity for pathogens to colonize the skin, potentially leading to skin disorders and infection.(Adebayo et al., 2020)

When under stress, microbes such as S. aureus can shift from simply being more abundant, to near-pathogenic, and release toxins that cause inflammation and aggravate the skin.(Geoghegan et al., 2018) This can lead to additional skin barrier impairment and a sustained flare.(Nature)(BYR 2018)

One way that can occur is through horizontal gene transfer (HGT) - the transfer of genetic material between microbes. In harsh environments, stressed bacteria might be more likely to acquire DNA from other bacteria through HGT events. This can result in the increased transfer of antibiotic resistance genes and/or genes that are associated with how successfully a pathogen can invade the body.(von Wintersdorff et al., 2016)

Exposure to toxic environmental factors can cause the expression of genes that promote pathogenic potential. Consequently, microbes that were once harmless may become harmful under these conditions.(Kaplan et al., 2016)

Safer Alternatives When There Is No Infection

S. aureus and other inflammation-loving species can sustain a flare, but their presence alone does not always lead to an infection. Please consult a doctor if you think you may have an infection

Then what can you do to support your microbiome and restore its natural immune controlling functions?

Creating a Healthy Environment Through Prebiotics & Probiotics

Emerging research points to the potential of prebiotics and probiotics in promoting a healthy skin microbiome and alleviating eczema symptoms.(NAK 2017)(KOH 2022) By incorporating prebiotic and probiotic supplements, individuals can support the growth of beneficial bacteria and fungi on their skin, leading to a more balanced and healthy microbiome.

Rulo’s Approach

At Rulo, we are microbiome aware in every ingredient that we use. We offer prebiotics and probiotics that have been shown to displace inflammatory microorganisms and restore a healthier microbiome. 

Understanding an individual's unique skin community can help tailor treatments that more effectively target the root cause of eczema.(KOH 2022) We also provide a test kit that can give you insights into your skin.

Gentle Cleansing

Avoid antiseptic and antimicrobial washes. Overdoing it can break the skin barrier and allow for the invasion of harmful bacteria and fungi.

See our washing article for more information.


Food avoidance diets have been shown to restore the microbiome to a more normal distribution.(SCO 2015) Adopting a healthier, anti-inflammatory diet can also help manage eczema symptoms.(PES 2021)

See our article on diet for more.


Understanding the complex relationship between the skin microbiome and eczema is crucial in providing effective treatments and improving the quality of life for individuals living with this chronic condition. By maintaining a balanced, healthy microbiome and addressing eczema triggers, one can experience relief from symptoms and lead a more comfortable life.

Explore our range of resources and articles to learn more about how ceramides can aid in the treatment and management of eczema.

Share your experiences with us! Tell us what has and hasn’t worked for you. What did we miss in this article that you've found personally impactful? Your insights can help others to better understand and manage their eczema.

About the Author(s)

Dr. Nicole Scott, PhD, MPH

Dr. Scott has published 29 peer-reviewed papers regarding human biology and the microbiome. Her work has been cited over 4300 times by other scientists.

She has battled eczema for most of her life and is the Founder of Rulo Skin.

Read her work on Google Scholar

Special Thanks

This article was prepared in collaboration with the Itchhikers Guide

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