The hygiene hypothesis links the growing epidemic of clinical manifestations of allergy, atopic eczema, allergic rhinoconjunctivitis and asthma to reduced exposure to microbes at an early age as a result of environmental changes in the industrialized world. These include improved sanitation and living conditions, vaccinations and antimicrobial therapy, together with declining family size and changes in dietary intake. The discovery of three subgroups of regulatory T cells has revolutionized the original immunological basis of the hygiene hypothesis, the so-called T helper 1/T helper 2 paradigm. In a case of defective oral tolerance allergy ensues. Recent experimental and clinical findings clearly indicate that both the development and maintenance of oral tolerance is dependent on these immunosuppressive regulatory T cells. Moreover, gut microbiota has been demonstrated to be crucial for the appropriate expression and function of the regulatory T cells, thus connecting microbiota closely to allergy. Indeed, many of the cross-sectional studies have shown a different composition of gut microbiota in children with atopic eczema and healthy controls. Most of the published prospective follow-up studies so far have also found that alterations in gut microbiota precede development of allergy. Changes in the amount of bifidobacteria, clostridia and Escherichia coli have been the most common findings in these studies. There has been, however, considerable variation in the settings of different prospective studies, making it difficult to interpret probable causes for variable results. The future studies addressing the issue should not only use novel molecular techniques of gut microbiota assessment, but also take into consideration several other aspects discussed in this paper.

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