The gut microbiota and allergy


Allergies have increased substantially within the past century, with a greater influence on those who live in developed Western countries. A number of theories and hypotheses have been proposed to figure out why this is occurring. One of the most well known is the Hygiene Hypothesis, proposed by David Strachan in 1989. This hypothesis assumed that the quality and quantity of bacterial organisms that the host encounters during the early period of life has an effect on the host’s immune system later on. Or in other words, the reduced exposure to bacteria could be the cause of the rapid increase in allergic disease. In a sense, he was saying that we have become “too clean”. 

The hygiene hypothesis however, is becoming less and less favoured due to the misconception that the population has about hygiene no longer being important. Hygiene is still very important, but the obsessiveness for sterilization and overconsumption of antibiotics are just some of the contributing factors resulting in the increase of allergies.

The association between allergy development and the gut microbiota has been studied immensely within the past decade. The gut microbiota is the bacterial population which inhabits our intestine and consists of trillions of microbial organisms that far outnumber our own body’s cells. It is estimated to consist of more than 500 bacterial species.

Results from a number of studies have demonstrated that the decrease in exposure to microbial organisms has resulted in a less diverse and underdeveloped gut microbiota, which has been associated with an increased risk of the individual devloping allergies later in life.

The exposure to a variety of environmental factors during infancy contributes to the development and diversification of the intestinal bacterial population which is the crucial time period for the establishment of a well functioning microbiota. Many environmental factors have displayed protective effects from developing allergic diseases.

The factors listed below play a key role in the initial colonization of the infant gut microbiota and the degree of risk for allergy development in the future.

Mode of delivery: Cesarean section vs. Natural birth. 

Infants delivered by Cesarean section have an increased risk of developing allergies later in life. The initial colonization of the gut resembles the mother’s skin microbiota and results in less diversification of the gut. In contrast, infants delivered naturally have a decreased risk of developing allergies. The initial colonization of the gut resembles the microbiota of the birth canal and results in higher diversity than infants delivered by C-section.

Probiotic intake during pregnancy

Maternal probiotic intake two months prior to birth and two months after birth during breastfeeding resulted in infants with higher diversity in the composition of their microbiota and reduced risk of developing allergies.

Mode of feeding: Formula vs. Breastfeeding

Infants who are breastfed receive probiotics from their mother’s breastmilk and are at a lower risk of developing allergies than infants who are formula fed.

Early antibiotic treatment

Infants who receive antibiotics within the first few years of life have an altered gut microbiota and display less diversity in the composition of their adult gut microbiota than those who did not receive antibiotics.

The presence of indoor pets, especially dogs, during the first few years of life has been demonstrated to reduce the risk of children developing allergies.

Prenatal farm exposure, or growing up on a farm has been demonstrated to be a factor which greatly reduces the risk of developing allergies.

Overall, the greater diversity of the gut microbiota during infancy, the less likely an individual will develop allergies. Further studies are being performed to determine a personalized approach for individuals and the prevention of future allergies.


Image 1:  Penn Medicine
Image 2: National Institutes of Health , Scientific American; Human Microbiome Project
Gollwitzer ES and Marsland BJ. 2015. Impact of early-life exposures on immune maturation and susceptibility to disease. Trends in Immunology [Internet]. [cited 2016 Oct 25]; 36(11): 684-696. DOI:
Marsland BJ and Salami O. 2015. Microbiome influences on allergy in mice and humans. Current Opinion in Immunology [Internet]. [cited 2016 Oct 20]; 36: 94-100. DOI:
Abrahamsson TR, Wu RY, Jenmalm MC. 2015. Gut microbiota and allergy: the importance of the pregnancy period. Nature [Internet]. [cited 2016 Nov 11]; 77(1): 214-219.  DOI: 10.1038/pr.2014.165
Matamoros S, Gras- Leguen C, Le Vacon F, Potel G, de La Cochetiere M-F. 2013. Development of intestinal microbiota in infants and its impact on health. Trends in Microbiology [Internet]. [cited 2016 Oct 3]; 21(4): 167-173. DOI:
Rachid R and Chatila TA. 2016. The role of the gut microbiota in food allergy. Current Opinion in Paediatrics [Internet]. [cited 2016 Nov 17]; 28(00): 1-6. DOI: 10.1097/MOP.0000000000000427
Schaub B and Vercelli D. 2015. Environmental protection from allergic diseases” From humans to mice and back. Current Opinion in Immunology [Internet]. [cited 2016 Oct 20]; 36: 88-93. DOI:

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