The Hygiene Hypothesis is too simplistic and the term has been abused and misinterpreted.
According to this theory, babies who are born in sanitised hospitals and come home to sparkling clean homes may be more prone to develop allergies.
It now seems unlikely that the maturation of a balanced immune system after birth would be driven primarily by bacteria that are harmful to the host.
From an evolutionary point of view, it is more likely that non-disease-causing microorganisms that have been present through the evolution of our immune system drive the process.
It has been suggested that modern living (a "western lifestyle") is associated with too little microbial stimulation early in life and that allergic and autoimmune disease could be a consequence of a "microbial deprivation syndrome".
Imbalance in gut flora
In terms of allergy, several studies show marked differences in the composition of the intestinal microflora of infants with and those without allergy.
These studies indicate an imbalance in the gut flora of allergic children and could suggest that differences in the indigenous intestinal flora might affect the development and priming of the immune system in early childhood.
Promising results have shown that probiotics could help to reduce infantile eczema. However, the European Academy of Allergy and Clinical Immunology concluded that evidence supporting the use of probiotics in the prevention and treatment of allergy is still preliminary.
It’s still hypothesis, but the potential effects of probiotics are probably strongest during the first years of life when immune regulation and oral tolerance develop.
Prof. Bengt Björkstén MD, PhD
Prof.em. of Paediatrics and Allergy prevention
Karolinska Institute, Stockholm, Sweden