The first clues that a baby may develop eczema or food allergies could be hiding in the microscopic organisms living on their skin, according to a new study led by researchers in Washington State University’s College of Veterinary Medicine. The work could eventually help clinicians identify at-risk children earlier and develop more personalized approaches to prevention and treatment.

Published in the journal Allergy, the study found that infants who later developed eczema or food allergies already showed changes in their skin microbiome long before any symptoms appeared. “We actually saw skin microbiome changes in infants who hadn’t even been diagnosed with these diseases yet,” said Zeyang Shen, assistant professor in WSU’s School of Molecular Biosciences and one of the study’s lead authors. “That was one of the most exciting findings because those changes could potentially be used as biomarkers to help clinicians diagnose disease earlier.”

Tracking More Than 1,000 Skin Swabs

Shen’s research focuses on the human skin microbiome, home to trillions of microorganisms, and its role in health and disease. This study focused on atopic dermatitis — commonly known as eczema, which can affect up to 20% of children — along with food sensitivities and food allergies. These conditions frequently appear during infancy and represent some of the earliest stages of the “atopic march,” a progression of allergic conditions that can later include asthma.

The team analyzed more than 1,000 skin swabs from 429 infants, collected at 2 to 3 months of age — before any diagnoses — and again at 12 months. Using advanced DNA sequencing, researchers identified the microbes living on the infants’ skin along with their genetic function. Infants who later developed eczema and food allergies showed microbial differences that predated any visible symptoms, and infants with eczema alone had different skin microbiome profiles than those who developed eczema alongside food allergies or sensitization.

The researchers also examined mutations in the FLG gene, one of the strongest known genetic risk factors for eczema, which helps produce a protein that keeps the skin’s protective barrier intact. Infants with eczema who carried FLG mutations had distinct skin microbiome profiles compared to noncarriers, hinting at a connection between genetics and the skin’s microbial community.

A Family Affair

The team also found substantial sharing of microbial strains between mothers and their infants. “The microbial strains are very much shared between infants and their mothers,” Shen said. “That gives us another layer to this story, suggesting that the people we live around and continuously exchange microbes with could also be contributing to our skin microbiome.”

Shen said future work will follow the same children as they age to investigate how early-life microbiome patterns relate to later health outcomes, including asthma and other allergic diseases. “Today, these diseases are diagnosed after symptoms appear,” he said. “If we can validate these microbial signals in other groups of children, they could potentially serve as early biomarkers that help identify disease risk much earlier.”

The study, “Shotgun Metagenomics Reveals Skin Microbiome Composition and Function in Infant Atopic Disease,” was published in Allergy (DOI: 10.1111/all.70449) and funded by the National Institutes of Health and the National Institute of Allergy and Infectious Diseases.