Allergies represent a condition where impaired immunological tolerance to common environmental allergens is the fundamental determinant of the disease. The immuno-pathological mechanism of the disease development is poorly understood. It is thought to involve complex genetic predisposition, which depending on environmental triggers and/or protective factors, may lead to allergic sensitization and development of allergic disease and the consequent symptoms (1-5). One environmental factor that has received particular interest in recent years is the variation in early microbial exposure, which has indisputable, although incompletely understood, effects on immunological maturation. Wider acknowledgment of the possible association between microbes and allergic diseases followed the introduction of what became known as "hygiene hypothesis" by Strachan, 1989 (6). Based upon epidemiological findings, he suggested that the rise in prevalence of allergic diseases in past decades was due to factors associated with changes in life style such as reduced family size and improved hygiene measures. He assumed that these epidemiological correlations reflected reduced opportunities for cross-infections in families with young children.

The basic idea linking microbes and allergies is that adequate microbial exposure may be able to direct the early immunological development away from allergic type responsiveness. In contrast, inadequate exposure does not provide this necessary stimulus and may even promote the development of allergic disease. The original hygiene hypothesis was based on infections, but what truly constitutes the characteristics and source of "adequate" microbial stimulus remains unknown. Intestinal microbiota are at least quantitatively the primary source of host-microbe interactions soon after birth. Moreover, the early establishment of the microbiota has been shown to be prerequisite for the formation of tolerance to mucosally encountered antigens (7-12). Arguably the best clinical evidence linking intestinal microbiota and allergies is provided by preliminary trials that have had success in preventing or treating allergic conditions by oral administration of intestinal bacterial isolates (13-18). Also, early use of antibiotics has been implicated to predispose the infant to allergic sensitization and development of allergic disease, although this view is controversial (19,20). The aim of this chapter is to summarize the current knowledge of the characteristics of gut microbiota in allergic infants and discuss their implication in allergic disease development.

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