The reason for the compositional differences in the average microbiota of allergic and healthy infants is not yet known. Undisputable conclusions regarding causal relationship cannot be drawn based on mere characterization of microbial composition relative to clinical sings and symptoms. In a few studies, characteristics of the fecal microbiota have been shown to precede the beginning of the expression of atopy, implying that these differences are not necessarily secondary to the disease. However, these, and other studies have not taken into account changes that occur in the development of the gut mucosa as these likely influence which microbes colonize and how these influence clinical signs of allergy.
Theoretically, there are a number of plausible causes for microbial compositional differences seen to date; these are listed in Table 1. Many of these factors are intertwined. Some plausible ways by which desirable microbes may protect the host from allergic sensitization and alleviate symptoms are presented in Figure 2.
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