How the microbiome affects the development of allergies


By Meghan Betts


Increasing evidence suggests that a disruption of the healthy human microbiome (i.e. communities of microbes, their genetic content and their interaction with the human host) is linked to an increased risk of developing allergic diseases.


Studies have shown that newborns who later develop either asthma or allergies commonly have a different composition of microbes in their guts (the gut microbiota) within the first few months of life compared to those who are unaffected by these disorders. There are many factors that can alter the composition of the microbiome in early life including:


Caesarean birth

Numerous studies have also shown that the mode of delivery (vaginal or caesarean) impacts the diversity of the microbiome. During a vaginal birth a baby encounters some of the first microbes that will colonise the gut from the mother. On the other hand, during a caesarean the baby is not exposed to these microbes and in addition encounters other microbes from the hospital environment. This alteration in the microbiota is believed to contribute to the development of allergy and asthma. One study in 2013 found that babies born by caesarean were 5 times more likely to develop allergies prior to turning two years old compared to babies born by vaginal delivery.

In an attempt to restore microbial diversity to caesarean-born babies, studies have swabbed newborn babies with the mother’s vaginal fluid. As unusual as this may seem, it has shown some success with the swabbed babies presenting with a gut microbiota more similar to those in babies born vaginally than babies who were not swabbed. This research is still in its early stages and more needs to be done to determine any risks of passing on pathological bacteria, but current results look promising.



In addition to the mode of delivery, an infant’s microbiota population is also impacted whether they are breastfed. One recent study showed that up to 28% of the infants microbiome comes directly from the mother’s breast milk, with an additional 10% from the skin on the mother’s breast. There is some evidence to suggest that breastfeeding protects against the development of allergies such as asthma, however research into this is still ongoing.



An emerging body of evidence suggests that exposure to pets at an early age may offer a level of protection from the later development of allergies and asthma. Originally it was believed that the protection conferred by early exposure to animals was due to desensitisation to potential allergens. However, new research suggests that the connection is linked to beneficial changes in the gut microbiome through exposure to a more diverse range of microbes. In particular, it appears that this is most effective prior to birth and during the first year of life.

Many epidemiological studies show that children who grow up in with regular contact with animals (i.e. on a farm or pets-owners) have a lower risk for developing allergies and asthma. As well as the presence animals themselves, other factors such as traces of soil that are brought in with them also contribute to an environment with a greater diversity of microbes.



Antibiotic use causes long term alterations to our gut microbiota and increasing evidence suggests that this is significantly associated with a rise in allergies. Dr Gary Huffnagle, University of Michigan, provided the first experimental evidence for the role of  antibiotics and microbes in the development of allergic airway disease. The study showed that an alteration of the gut microbiota following a course of antibiotics caused an increased hypersensitivity and reactivity in the lungs of mice in response to harmless yeast spores. In particular, antibiotic use during the early years of life is shown to significantly impact the risk of childhood atopy (a genetic tendency to develop allergic diseases), in particular sensitivity to food allergens.



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