Infant gut fungi linked to childhood allergy and asthma risk
Two Nature Communications studies point to gut fungi, including Malassezia, as possible targets for preventing pediatric allergic disease.
By Priya Raghavan · Science Reporter
3 min read
Two studies published in Nature Communications report that fungi in the infant gut are tied to immune development and the later risk of allergic disease. The findings matter because they point to the gut mycobiome, a less-studied part of the microbial community, as a possible target for preventing conditions such as allergic asthma, food allergy and atopic dermatitis.
The papers focused on the fungal organisms that live in the gut, known collectively as the mycobiome. Researchers have studied gut bacteria far more extensively, but the two teams said fungal communities may also shape immune function during a narrow early-life period.
One study, led by Dr. Stuart Turvey and colleagues at BC Children's Hospital Research Institute, analyzed data from the CHILD Cohort Study. According to the paper, the team examined 2,256 stool samples from 1,409 participants during the first year of life to track how fungal communities changed as infants developed.
Turvey’s group reported that different fungal families followed distinct patterns over time. Saccharomycetaceae became more common across the first year, while Malassezia declined, according to the study.
Fungal patterns tied to later allergy
The BC Children's Hospital Research Institute team also found links between the presence of certain fungi in infancy and allergic conditions diagnosed by age 5. In one example reported by the researchers, Malassezia appeared more often in infants who later developed atopic dermatitis.
Turvey, an investigator at BCCHR and a professor of pediatrics at the University of British Columbia, said in the University of Calgary release that allergic diseases affect hundreds of millions of children worldwide and are becoming more common. He said better knowledge of how those diseases begin could help efforts to prevent them.
A second study, led by Dr. Marie-Claire Arrieta and colleagues at the Snyder Institute for Chronic Diseases and the Alberta Children's Hospital Research Institute at the University of Calgary, examined how antibiotic treatment affects the infant mycobiome. The researchers studied infants younger than six months in a prospective clinical study, then followed up with mouse experiments.
Arrieta’s team reported that antibiotics increased fungal species in the infant gut, especially Malassezia. In mice, the researchers found that colonization with that fungus increased allergic inflammation in immune cells in the gut and airways, according to the paper.
Antibiotics and the developing immune system
The University of Calgary team said the findings suggest a pathway by which antibiotic exposure early in life could alter fungal communities and affect allergic disease risk. Arrieta said in the university release that antibiotics remain essential for young children when medically needed, while the study points to an overlooked effect on gut fungi.
Taken together, the two papers place Malassezia at the center of a possible connection between early gut development and allergic immune responses. The researchers said the infant mycobiome could become a target for therapies aimed at preventing immune dysregulation and pediatric allergic disease, though the studies do not report a tested treatment for children.
The papers are titled “Saccharomycetes and Malassezia fungi associate with early-life gut maturation and allergic disease risk in childhood” and “Antibiotic-induced Malassezia expansion in the infant gut promotes early-life immune dysregulation and airway inflammation in mice.” Both were published in Nature Communications in 2026.
This story draws on original reporting from Medical Xpress.