ABOVE: Researchers used wildling mice housed under seminatural conditions to study the effects of exposure to a diverse set of microbes on allergic inflammation. Benjamin Tull

Modern societies evolved to be very sanitized, and even the idea of living in unclean environments unsettles most people. This rise of ultraclean societies came with an uptick in allergies, and researchers thought that the lack of exposure to a diverse microbial community, which could educate the immune system to respond adequately when exposed to allergens, was to blame. Now, in a Science Immunology study, researchers described how harboring a diverse set of microbes does not protect mice from developing strong allergic responses.1 Their findings call into question the idea that the lack of microbial exposure is the primary factor driving the rise in allergies.   

It was an interesting model system and a comprehensive study looking at allergic responses. I appreciated the lengths that they have gone to to create that system and their efforts to get closer to the human experience.
-Sara Hamilton, University of Minnesota

“It adds to what we already appreciated was a very complex situation,” said Sara Hamilton, an immunologist at the University of Minnesota who was not involved in the research. “It was an interesting model system and a comprehensive study looking at allergic responses. I appreciated the lengths that they have gone to to create that system and their efforts to get closer to the human experience.”

According to the hygiene hypothesis, which gained a foothold around 1990, infections and exposure to a variety of microbes, especially during early life, could protect against the development of allergies. Epidemiological studies around that time further supported the idea, showing for example, that children raised on farms and therefore more likely to be exposed to an array of microbes were less likely to develop asthma and other allergic diseases.2,3 Despite the evidence, these studies often failed to control for other environmental factors, leaving scientists to wonder if microbes alone were responsible for the observed protective effects against allergies. 

As a researcher who studies the interplay between genes and the environment on immunity, Jonathan Coquet, an immunologist at the University of Copenhagen and author of the paper, was curious to know if microbes really contribute to the development of allergies. To study this question, he needed a mouse model since the laboratory setting allows better control of those other environmental factors. However, commonly used (very clean) laboratory mice did not seem ideal for tackling the problem, as these animals have less diverse microbiomes than mice in the wild.

In his search, Coquet came across a mouse model developed by Stephan Rosshart, a microbiome researcher and clinician at the University Hospital Erlangen and coauthor of the study. For this model, Rosshart and his colleagues transplanted mouse embryos from a commonly used laboratory mouse strain into wild surrogate mouse mothers, which gave birth to newborn pups referred to as wildlings. Even though the wildling mice were genetically similar to standard laboratory mice, they acquired a richer whole-body microbiota that resembled that of wild mice.4

For the present study, Coquet and Rosshart teamed up with an international group of researchers to determine whether long-term exposure to a variety of microbes would protect mice from developing allergic immune responses. The scientists used specific pathogen free (SPF) mice and wildling mice for their experiments. While the researchers housed the SPF mice in standard laboratory conditions, they supplemented the cages of wildlings with hay, compost, and particles from wild mice, ensuring a lifelong exposure to diverse microbes.  

The team then exposed SPF and wildling mice to various allergens, including house dust mite extract, an airway irritant fungus (Alternaria alternata), and a recombinant IL-33 cytokine, a molecule that stimulates immune cells. Following the allergen challenge, the researchers examined a range of cytokines and immune cells in the lungs and serum at different time points.

Wildlings showed robust airway inflammation in response to the allergens, in contrast to what the hygiene hypothesis predicted. Specifically, these mice developed a strong type two immunity, the typical adaptive response to allergens seen in people with allergies, characterized by the presence of T helper 2 cells. Six weeks of allergen exposure induced similar allergic inflammation in SPF and wildling mice, suggesting that even with prolonged allergen exposure, the wildling microbial enriched environment did not protect the animals against the development of allergic responses. 

“It was pretty striking how similar it was between the two groups of animals,” said Hamilton, who was surprised that the wildlings showed no dampening of their allergic immune responses when challenged with the allergens. Rosshart explained that the findings would have surprised most researchers. “If you asked 100 scientists upfront, the overwhelming majority of scientists would have thought ‘okay, probably the wildling mice will have fewer symptoms, fewer allergies, less inflammation, or they might even be protected,’” he said. “This made the study actually cool because it was different from what people expected.”

While the present work focused on airway allergens, Hamilton believes that an interesting next step would be to assess the wildling mouse responses to allergens administered through the skin or other routes, an idea that Coquet plans to explore.

Meanwhile, Coquet is excited that researchers are paying attention to the findings and questioning more established ideas in the allergy field. “The hygiene hypothesis has really captured the public's imagination for 35 years or longer. It's quite easy to grasp as a concept, made some sense, and is backed by some data,” he said. “It is exciting that people may start to question it and get a different perspective. That's great for science. That's great for the public, that you can instill and help people question some fundamental notions of life or of why they might have allergies themselves.”


  1. Ma J, et al. Laboratory mice with a wild microbiota generate strong allergic immune responses. Sci Immunol. 2023;8(87):eadf7702.
  2. Riedler J, et al. Exposure to farming in early life and development of asthma and allergy: a cross-sectional survey. Lancet. 2001;358(9288):1129-1133. 
  3. Kilpeläinen M, et al. Farm environment in childhood prevents the development of allergies. Clin Exp Allergy. 2000;30(2):201-208. 
  4. Rosshart SP, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019;365(6452):eaaw4361.