Results obtained by molecular-based culture-independent techniques are largely supportive of the findings presented above. In another prospective follow-up, the fecal microbiota in Finnish neonates was studied prior to the expression of atopy as detected by a positive skin prick test at year one (n = 12). The microbiota of these sensitized children tended to contain lower numbers of bifidobacteria and significantly higher numbers of Clostridium histolyticum than those in samples from infants with a negative prick test (n= 17) (48). The Clostridium species detectable with the oligonucleotide-probe used in that study include common infant gut colonizers such as C. paraputrificum, C. butyricum and C. perfringens but not C. difficile. However, another study indicated that relatively high fecal levels of rarely detected i-caproic acid indicative of C. difficile activity was associated with presence of IgE mediated allergic condition in Swedish infants at around one year of age (49). The association between low numbers of fecal bifidobacteria and subsequent allergic sensitization was confirmed in a study showing that neonatal bifidobacteria numbers were significantly lower in children who had food allergen-specific IgE antibodies in their serum at 2 years (n= 10) than in those who did not have the antibodies (n= 16) (50). In addition, the numbers of bifidobacteria present during the neonatal period correlated inversely with total IgE concentration at 2 years (n = 25). In accordance with the association suggested by the earlier studies between the high prevalence of coliforms and allergy, another study showed a direct correlation between the fecal numbers of Escherichia coli and total IgE concentration in infants with early onset atopic eczema at mean age of 5 months (n= 19) (18). Furthermore, at weaning around 1 year of age total bacterial cell counts correlated inversely with the severity of eczema as indicated by severity Scoring Atopic Dermatitis (SCORAD) scores (44).
Somewhat contrasting results to those presented by plate culture methods have also been reported. In a study of 6-month-old exclusively breast-fed infants the mean bifidobacterial numbers were not found to be lower in the feces of infants with early onset atopic eczema (n=15) compared to controls (n=10), with the exception of a small subgroup of allergic infants (n = 5) that additionally had gastrointestinal symptoms. Moreover, as opposed to studies by Bjorksten and co-workers, Bacteroides numbers were higher in a subgroup of allergic infants (n = 6) who were later confirmed to have cow milk allergy by challenge (44). Bacteroides numbers were also associated with cow milk allergy in a later study where the high counts correlated directly with serum total IgE concentration in a subgroup of infants intolerant to extensively hydrolyzed whey formula (n = 7) (18).
During weaning, the numbers of Clostridium histolyticum correlated inversely with the severity of atopic eczema as indicated by SCORAD scores whereas lactobacilli/ enterococci numbers correlated directly with the serum total IgE levels (44). It is worthy of note that although high total IgE concentration represents phenotypic characteristics associated with an atopic background, unlike allergen-specific IgE antibodies, the immunopathophysiological significance of total IgE is questionable (51).
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