The Skin Microbiome & Diaper Rash: The Science Parents Should Know

Chronic diaper rash or “extra-sensitive” skin can be a clue that your baby’s skin microbiome is out of balance. Here’s what that means—and what actually helps.

What is the skin microbiome?

Your baby’s skin is home to a living community of microbes (mainly bacteria and fungi) that help defend against irritants and support a healthy skin barrier. 

In early life, this ecosystem is still maturing and is shaped by factors like birth mode, environment, moisture, pH, and skin care product choices.

RECOMMENDED: From Day One: How the Baby Skin Microbiome Shapes Lifelong Health

What does an unhealthy skin microbiome look like?

When the skin microbiome’s army of protective microbes is too low, bacteria and fungus can more easily find their way in. As a result, skin can become drier, redder, and more reactive, and inflammation is easier to trigger. 

On infant skin, dysbiosis (microbial imbalance) is linked to barrier weakness and inflammatory skin conditions.

Why the diaper area is vulnerable

The diaper region is warm, moist, and exposed to urine and stool—conditions that change skin pH and activate fecal enzymes that can damage the barrier and shift the local microbiome.

Friction from diapers can cause tiny abrasions that make it easier for infections to set in and spread.

That’s why the diaper area is the most common site of rash in infancy.

What bacteria (and yeast) cause diaper rash in infants?

• Candida albicans (yeast) frequently overgrows in rashes lasting >3 days.
• Staphylococcus aureus and Streptococcus pyogenes (bacteria) can cause or complicate rashes.

The microbiome–rash loop

Newer studies show the diaper-area microbiome shifts during rash, which fuels inflammation and slows healing—a cycle that can make rashes repeat or even be chronic. 

The gut-skin axis: Advancements in diaper rash research

You may have heard about probiotics helping with digestion—but scientists are now discovering that the gut and skin are more connected than we once thought. This link, known as the gut–skin axis, describes how the community of microbes in the digestive tract can influence skin health, immunity, and inflammation throughout the body.

Early research shows that gut microbes produce metabolites and signals that can affect the skin microbiome, the barrier function, and even how the skin responds to irritation or infection. 

In infants, this connection is especially fascinating because both the gut and skin microbiomes are still developing together during the first year of life.

Can probiotics help prevent or treat diaper rash?

There’s no single probiotic proven to prevent or treat diaper rash yet, but research exploring the gut–skin axis suggest that balancing gut bacteria could help improve skin conditions by reducing systemic inflammation and supporting a healthier skin barrier.

Some parents already choose to use infant probiotics in hopes of reducing rashes or digestive issues, but research hasn’t identified one specific strain or product that consistently helps. 

If you want to try probiotics, be sure to check with your pediatrician first.

Best practices: Caring for your baby’s skin microbiome (and preventing rash)

1) Cleanse gently (not aggressively).

Skip the harsh wipes and soapy cleansers—these can strip the skin’s protective oils and disrupt its microbiome. Instead, use a gentle, oil-based cleanser that lifts away stool and urine without over-cleansing.

2) Minimize friction and trapped moisture.

Pat (don’t rub) the skin dry and give it time to breathe whenever possible. Even a few minutes of diaper-free time can help the skin reset.

3) Rebuild and protect the barrier.

Apply a barrier cream at each diaper change and after baths—especially during flare-ups—to reduce contact with moisture and irritants.

4) Be mindful of triggers that shift the microbiome.

Antibiotics, new detergents, or overly frequent washing can all disrupt the balance of good bacteria. Stick to a simple routine with a few trusted, fragrance-free products.

When to call the pediatrician

• Rash persists beyond 3–4 days, is very painful, or is associated with fever, pus, open sores, or bright-red ring around the anus (possible bacterial infection).
  
• If your baby is younger than 2 months, preterm, or has underlying medical issues, get personalized guidance sooner.

Rash & Skin Microbiome FAQs

What is the skin microbiome?

The community of microbes living on skin that helps defend against irritants and supports barrier and immune health—still developing in infancy.

What bacteria causes diaper rash in infants?

Rashes are often multifactorial. Candida albicans (yeast) commonly overgrows in prolonged rashes; Staphylococcus aureus and Streptococcus pyogenes can also be culprits or complicating factors. 

What does an unhealthy skin microbiome look like?

More redness, dryness, and rash or eczema flare-ups.

Can probiotics help with diaper rash?

Possibly, but the science can’t tell us which probiotic strains are best yet. Ask your pediatrician before trying supplements. 

Baby skin microbiome: how can I support it day-to-day?

Gentle cleansing with water or non-soap cleansers, fragrance-free products, frequent changes, and skin barrier protection.