June 24, 2026, 6:11 pm | Read time: 5 minutes
In recent years, numerous studies have shown how important the gut is for our health. The influence of gut bacteria on bodily functions is extremely high, affecting not only digestion but also the immune system and even the brain. Two new studies indicate that certain fungi in the gut may influence whether we develop allergies.
According to a scientific report by the Federal Institute for Risk Assessment, more than 30 percent of people in Germany develop an allergic disease during their lifetime.1
This involves a disruption in the immune system, causing it to overreact to certain foreign substances. These can include plant pollen, medications, chemicals, and foods, leading to symptoms like itching, redness, and swelling. Two new studies show that a specific type of fungus in children’s guts may play a key role in the development of allergies such as eczema and asthma.
What exactly did the two studies investigate?
The first study is by Dr. Stuart Turvey and his team at the Canadian BC Children’s Hospital Research Institute (BCCHR) in Vancouver.2 They analyzed data from the large-scale CHILD Cohort Study, which scientifically monitors the development of over 3,500 children. For this investigation, 2,256 stool samples from 1,409 children in their first year of life were evaluated. The researchers aimed to identify which fungi colonize the gut in early infancy and whether there are links to the later development of allergic diseases such as eczema or food intolerances in children up to the age of five.
In the second Canadian study, led by Dr. Marie-Claire Arrieta from the Snyder Institute for Chronic Diseases and the Alberta Children’s Hospital Research Institute at the University of Calgary, a different approach was taken. The researchers prospectively examined how antibiotic treatments in infants under six months affect the gut microbiome and what immunological consequences this may have.3
Additionally, mouse experiments were conducted to demonstrate causal relationships in the lab. Notably, the two studies complement each other, thereby reinforcing their respective findings.
Fungal Species Follow Different Developmental Paths
The analysis of data from the CHILD Cohort Study by Dr. Stuart Turvey and his team revealed that different fungal species in the infant gut exhibit characteristic developmental patterns. For instance, the Saccharomyces family (also known as sugar yeasts) increased steadily in the first year of life, while the Malassezia genus (also a yeast) showed the opposite trend. Crucially, the prevalence of individual fungal species was linked to later immunological diseases. Malassezia, for example, was more frequently detected in infants who developed eczema during childhood.
“Hundreds of millions of children worldwide are affected by allergic diseases, and the number is rising,” comments Dr. Stuart Turvey on the results of his study. A better understanding of the causes of these diseases and ways to prevent them would be of enormous benefit to children around the world.
Antibiotics Shift the Fungal Balance
But what leads to an unhealthy gut flora or a fungal imbalance? The second study by Dr. Marie-Claire Arrieta provides an answer. Her research team showed that antibiotic treatment in early infancy measurably increases the number of fungal species in the gut, particularly the yeast Malassezia. This species is associated with the development of eczema. Subsequent mouse experiments revealed that colonization with this fungus leads to an increased allergic inflammatory response in immune cells of the gut and airways.
“These findings uncover a previously unknown link between antibiotic use in early childhood and the risk of allergic diseases, showing how the developing immune system is shaped by fungi in the gut microbiome during a critical developmental phase,” explains study leader Dr. Arrieta in a press release.4
While antibiotics are often an indispensable treatment for young children, her study shows that there is a previously overlooked effect on the gut microbiome. Antibiotics can promote the growth of fungal species like Malassezia, directly influencing immune function.
This research highlights a previously often overlooked part of our gut flora: the mycobiome. While the role of bacteria is well-researched, these new data show that fungi like Malassezia play a crucial role in shaping our immune system. Since antibiotics remain vital in emergencies, these insights could help develop accompanying therapies in the future to protect the fungal balance in the gut during treatment.
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Both studies show how certain fungal species in the gut may influence whether we develop allergies. According to the researchers, the yeast Malassezia is particularly associated with the development of eczema and asthma. This insight could help develop new therapeutic approaches in the future. Additionally, a more conscious use of antibiotics could help avoid excessive fungal growth during this critical phase.
Future studies could help develop new treatments for allergies, such as preventing the spread of the Malassezia fungus in the gut.
Assessment of the Studies and Possible Limitations
The studies have several strengths: The first is based on many participants, and the second complements the results with various investigations, allowing for a more precise examination of possible biological connections.
However, there are also limitations: The first study only shows correlations and cannot prove that the fungi are actually the cause of the diseases. Results from mouse experiments provide important clues but cannot always be directly applied to humans.
Additionally, there is a lack of information on risk numbers, effect sizes, and follow-up periods, making the actual significance of the results only partially assessable.