Over 10% of children in the United States suffer from chronic eczema[1], yet parents are often advised that eczema is not only common, but a normal childhood condition that their child will simply outgrow. Children are often prescribed topical steroid creams and antibiotics to manage their inflamed skin. However, this surface-level approach ignores a crucial question: What if eczema is a warning sign of a deeper issue? As functional practitioners, we must look beyond the skin, and view the outward presentation of eczema as a signal of an inflamed gut and an angry immune system. Our role is to course correct the health of the internal terrain by identifying and addressing the root cause.

Early Colonizers

Insufficient colonization by beneficial bacteria early in life leaves children vulnerable to several gut issues that can lead to eczema. Without a robust microbial balance, children have an increased susceptibility to reduced mucosal health, poor immune function, slow motility, inflammation in the gut lining, and intestinal permeability that can lead to eczema[2]. Research indicates that young children with eczema frequently exhibit reduced abundance of early colonizers, such as Bifidobacterium, or microbial diversity, increasing risk for development of eczema.[3] Without the protection provided by these early colonizers, a child’s gut microbiome is more susceptible to proliferation of dysbiotic bacteria, including Clostridium and Staphylococcus species.[4]

When a child’s early microbial colonizers are reduced in abundance, Staphylococcus and Streptococcus species often become prevalent, further contributing to the inflammation seen in children with eczema. These microbes not only increase the risk of skin infections in eczema, but can affect other mucosal areas, such as the sinuses and lungs, frequently leading to sinus and ear infections. While antibiotics are a common treatment route for these concurrent issues, early life antibiotic exposure has been shown to increase risk for developing eczema by depleting a child’s microbiome, reducing the function of its first line of defense against proliferation of dysbiosis and fungal growth.[5]

Microbes Gone Awry

We know that an imbalanced gut and skin microbiome and inflamed terrain creates an environment for dysbiotic bacteria to flourish. Many of these bacteria, such as Klebsiella and Pseudomonas species, are histamine producers, increasing the body’s histamine load. The heightened histamine output at baseline drives the cycles of a child’s persistent itching and scratching, compromising the skin barrier and increasing susceptibility to opportunistic microbial colonization.

Eczema in children often presents in areas prone to moisture, such as the backs of the knees, insides of the elbows, neck, wrists, and ankles. This specific presentation suggests a potential underlying issue in the gastrointestinal tract such as Candida overgrowth or even mold colonization within the mucosal linings of the body, including the gut. Fungal species are opportunistic and flourish in moist conditions, not as a primary cause but when the body’s protective terrain is compromised. A healthy terrain is protected by intact mucosal linings, a balanced immune response, and an adequate commensal microbiome.[6]

Leaky Barriers

Eczema, presenting as an inflamed and damaged skin barrier, is fundamentally a reflection of internal health, particularly a compromised gut. A “leaky gut” or increased intestinal permeability allows harmful substances like toxins, microbes, and food antigens to breach the gut barrier and enter the bloodstream. This creates a systemic pathway for inflammatory compounds to travel throughout the body.

Furthermore, when the body’s primary elimination pathways are not functioning optimally, as we see in childhood constipation, the skin may become an easy secondary exit route for waste. Therefore, to effectively heal the skin barrier and resolve eczema, the approach must include repairing and sealing the gut barrier. Many families don’t see success with topical approaches long term because eczema is not simply a topical skin issue; it is an internal health problem rooted in intestinal barrier dysfunction and an immune system that has become overreactive due to chronic exposures.

The immune system is inherently intelligent, responding to substances perceived as foreign or unusable. Similar to the gut, a compromised skin barrier allows the entry of chemicals, toxins, microbes, and other irritants. Children are especially vulnerable to leaky barriers as their immune system continues to develop and their gut barrier continues to strengthen.

Identifying the Problem

We always start with a gut-forward approach by identifying the balance of microbes in the gastrointestinal tract, sources of inflammation that may contribute to further intestinal permeability, and intestinal health function such as immune response and digestive factors. Furthermore, early life exposure to mold and mycotoxins can significantly disrupt the microbiome. Mold is known to suppress the immune system, impede detoxification, and slow elimination—often causing constipation. This, in turn, allows for the greater circulation of microbes and toxins.

To successfully rebalance the internal health of the child and resolve eczema, we must identify and address the underlying factors and root causes with a targeted, step-wise approach. Utilizing functional labs, such as a GI-MAP and mycotoxin testing, we aim to answer the following questions:

1. Are there any pathogens contributing to an inflamed GI tract and presence of chronic eczema? Enterohemorrhagic E. coli or Clostridium difficile, for instance, have been associated with pediatric eczema [7].
2. Is the beneficial microbiome robust and balanced enough to ensure opportunistic bacteria and fungal species are unable to proliferate?
3. Is there evidence of dysbiotic bacterial, fungal, or parasitic overgrowth? Specifically, are any of these opportunistic organisms producing inflammatory compounds, such as histamine, in the gut that could increase the itching and discomfort associated with eczema?
4. Is digestive capacity sufficient to effectively break down food proteins to optimize nutrient absorption and immune function?
5. Is the stability of gut immune function compromised? Has chronic exposure to microbes, toxins, and food antigens led to its depletion? Or, is the immune system hyper-vigilant, sounding the alarm in response to a variety of inflammatory factors and antigens?
6. Is there evidence of overt inflammation in the GI tract, suggesting damage to the gut barrier and increased risk for atopic or allergic presentations?
7. Is mold colonization or mycotoxin exposure a factor to consider? Mold exposure may be disrupting the immune system, damaging the gut lining and other mucosal barriers, and contributing to an unhealthy gut terrain. If you suspect mold and mycotoxins may be an issue, refer out to a Master Restorative Health Practitioner who can provide appropriate and strategic detoxification support for the child.

At the Institute of Restorative Health, we equip you with the tools and expertise to assess the root causes of gut and skin dysfunction in children and adults, and develop effective solutions for healing.

Developing the Solution

When it comes to addressing the gut microbiome for children, a probiotic is simply not enough. We frequently identify extremely high levels of overgrowth of dysbiotic bacteria or Candida, gut immune depletion, and intestinal permeability in children with eczema. Successfully rebalancing the gut requires a comprehensive approach to address eczema from the internal terrain.

1. Nourish: A healthy diet rich in nutrient-dense whole foods is critical. A child’s consumption of inflammatory processed foods can exacerbate microbiome imbalances and contribute to intestinal permeability. Since food sensitivities are common in children with eczema, a comprehensive food sensitivity test like the MRT-176 can help identify inflammatory food triggers without eliminating entire food groups important for growth and development.
2. Support digestion & bile: Use enzymes and biliary support to ensure proper nutrient utilization and minimize immune dysregulation. While HCl isn’t used in children, support a parasympathetic state at meals (calm, seated environment). Address elimination via adequate liver and biliary function for motility—often compromised by microbes or mold exposure.
3. Repair the lining: Utilize gut-supportive nutrients such as L-glutamine, aloe, butyrate, and immunoglobulins to aid repair cycles, reduce permeability, and support immune regulation.
4. Rebuild the microbiome: For pediatric eczema, consider both spore-based and transient strains. Spore-based (e.g., Bacillus species; Saccharomyces boulardii) can help rebalance post-antibiotic use; transient strains (e.g., Bifidobacterium, Lactobacillus) are valuable when early colonizers are insufficient.
5. Address overgrowths (as indicated): Gentle antimicrobial/antifungal support can target biofilms, bacteria, and yeast that disrupt immune function and inflame the gut, reducing inflammatory byproducts and protecting skin/gut barrier integrity.
6. Bind & clear: Select binders (as appropriate) to limit recirculation of toxins and die-off byproducts so eradication can be mild—even symptom-free—while supporting GI elimination.

While addressing the underlying root causes of pediatric eczema, prioritizing the child’s comfort is essential to improve their quality of life during a healing protocol. While many parents have tried a wide array of topical medications and moisturizers, a “less is more” approach can be surprisingly effective. To support the skin barrier’s healing and preserve the natural, healthy skin microbiome, minimize baths and the use of soaps. Pairing just one to two targeted topicals can support the skin barrier without adding excessive moisture, which is especially important in cases of fungal eczema. A potent combination to keep dryness and itching under control is applying a hypochlorous spray to open or cracked areas to prevent secondary bacterial infections, followed by a gentle, skin-friendly oil or balm, such as jojoba oil.

Children with eczema frequently suffer from intense itching, often leading to further damaging the compromised skin barrier, which potentially introduces bacteria into open micro-wounds. A common contributing factor can be low histamine tolerance or excessive levels of histamine in the body due to underlying infections, like microbial overgrowth in the gut. In such cases, any stressor on the body can exacerbate itching, such as food sensitivities, lack of sleep, or even excitement. When a child is itching frequently, providing histamine support can be helpful. Natural plant compounds like quercetin and perilla extract can offer histamine and mast cell stabilizing, and can be used effectively alongside a healing protocol.

Changing the Trajectory of a Child’s Life

Parents watch their children suffer with this cascade of inflammation, marked by incessant itching and uncontrollable scratching, which allows the skin barrier to become more inflamed. While topical treatments offer temporary relief, lasting improvement requires the crucial work of rebalancing the microbiome and repairing both the skin and intestinal barriers.

Not only does supporting eczema from a gut-first approach offer relief for inflamed itchy skin in the short term, but by rebalancing the microbiome and relieving the immune system of dysfunction, practitioners can set the stage for improved outcomes long term with reduced risk of a cascade of concerns, such as allergies, asthma, and even ADHD. With eczema, parents have a visual barometer of their child’s health, but it’s the improved quality of life for the child that makes the journey of healing eczema that much more profound for the entire family.

References

1. Zablotsky, B., Black, L. I., & Akinbami, L. J. (2023, January). Diagnosed allergic conditions in children aged 0–17 years: United States, 2021 (NCHS Data Brief No. 459). National Center for Health Statistics. https://www.cdc.gov/nchs/data/databriefs/db459.pdf
2. Tang H, Li W, Xu Y, Zhou Y, Hamblin MR, Wen X. Gut microbiota modulation: a key determinant of atopic dermatitis susceptibility in children. Front Microbiol. 2025 Apr 28;16:1549895. doi: 10.3389/fmicb.2025.1549895. PMID: 40356648; PMCID: PMC12066585. https://pmc.ncbi.nlm.nih.gov/articles/PMC12066585/
3. Zhang Y, Jin S, Wang J, Zhang L, Mu Y, Huang K, Zhao B, Zhang K, Cui Y, Li S. Variations in early gut microbiome are associated with childhood eczema. FEMS Microbiol Lett. 2019 May 1;366(9):fnz020. doi: 10.1093/femsle/fnz020. PMID: 30860574. https://pubmed.ncbi.nlm.nih.gov/30860574/
4. Liu, Y., Du, X., Zhai, S., Tang, X., Liu, C., & Li, W. (2022). Gut microbiota and atopic dermatitis in children: A scoping review. BMC Pediatrics, 22, Article 323. https://doi.org/10.1186/s12887-022-03390-3
5. Tsakok T, McKeever TM, Yeo L, Flohr C. Does early life exposure to antibiotics increase the risk of eczema? A systematic review. Br J Dermatol. 2013 Nov;169(5):983-91. doi: 10.1111/bjd.12476. PMID: 23782060. https://pubmed.ncbi.nlm.nih.gov/23782060/
6. Jawhara S. How Gut Bacterial Dysbiosis Can Promote Candida albicans Overgrowth during Colonic Inflammation. Microorganisms. 2022 May 12;10(5):1014. doi: 10.3390/microorganisms10051014. PMID: 35630457; PMCID: PMC9147621. https://pubmed.ncbi.nlm.nih.gov/35630457/
7. Penders J, Thijs C, van den Brandt PA, Kummeling I, Snijders B, Stelma F, Adams H, van Ree R, Stobberingh EE. Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study. Gut. 2007 May;56(5):661-7. doi: 10.1136/gut.2006.100164. Epub 2006 Oct 17. PMID: 17047098; PMCID: PMC1942165. https://pmc.ncbi.nlm.nih.gov/articles/PMC1942165/

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Julia Mims

FNTP, MRHP

As a college student majoring in Nutrition and navigating her own health journey, Julia began to explore the world of functional health, ready to move forward into a career in holistic nutrition. She became a Functional Nutritional Therapy Practitioner in 2017, and continued her training with the Institute for Restorative Health beginning in 2020. Since then, she has utilized the IRH methods as a Master Restorative Health Practitioner in her work in the pediatric space, where she supports the healing journeys of children who experience challenges with eczema, allergies, asthma, ADHD, and autism. Julia is the senior pediatric specialist with the Always Growing Wellness team. Outside of working with families and instructing with the IRH, She is the mother of two beautiful children, and enjoys spending time with her husband and kids in their small town community.