In the present paper we combined two culture-independent molecular approaches, HTF-Microbi.Array and qPCR, for a pilot characterization of the atopy-associated dysbiosis of the intestinal microbiota in 19 atopic children living in Italy. At high phylogenetic level both atopics and controls showed a comparable overall microbiota profile where Firmicutes and Bacteroidetes constituted the two dominant divisions. However, focusing at lower taxonomic level, the intestinal microbiota of atopic children was characterized by a significant depletion in members of the Clostridium cluster IV, F. prausnitzii, A. muciniphila and a corresponding increase of the relative abundance of Enterobacteriaceae.
In a case–control DGGE-based study of the faecal microbiota from 20 allergic and 20 non-allergic 5-year-old Estonian children, Stsepetova et al.
] reported a less diverse composition in the faecal microbiota from atopic children but, according to the Authors, no bacterial targets could distinguish infants with or without atopy. However, the DGGE-based approach allowed to consider only the dominant fraction of the intestinal microbiota, remaining blind with respect to the whole phylogenetic complexity of the ecosystem. In an elegant 16
S rDNA pyrosequencing-based dynamic study, Hong et al.
] addressed the differences in the microbiota succession between 3 infants with and 4 without eczema over four time points until 24
months of age. Even if age was shown to be the dominant factor mediating microbiota changes, matched by age eczema infants were characterized by a higher abundance of the enterobacteria Klebsiella
as well as Enterococcus
, while Bifidobacterium
showed a higher abundance in non-eczema ones. These last data are in general agreement with the intestinal microbiota dysbioses observed in our study.
have been traditionally indicated as possible protective factors against atopic disease in childhood [16
], we did not detect any significant differences in these health-promoting genera between atopics and controls, confirming previous findings reported by Penders et al.
]. However, molecular studies at the species level showed a different distribution of the Bifidobacterium
species between allergic and non-allergic children [36
], suggesting a potential species-specific effect of Bifidobacterium
in the etiology of atopic disorders.
The atopy-related microbiota dysbioses we depicted in our cohort of 19 children were independent of their peculiar allergic profile. A subset of 10 atopics underwent clinical evaluation of total IgE level and the correlation between IgE and the relative abundance of specific microbial groups in the faeces was explored. Even if no significant correlation was determined, L. casei et rel.
cluster IX tended to be negatively and positively correlated with IgE, respectively. Interestingly, Ogawa et al.
] demonstrated that orally administered L. casei
was effective in the control of the IgE levels in human allergic reactions and, recently, Schiffer et al.
] reported that L. casei
could inhibit the effector phase of immune inflammation in vivo
. Finally, Penders et al.
] showed a decreased risk of atopic dermatitis in children colonized by L. paracasei
, a member of the L. casei et rel.
group. Even if these studies may support the tendency towards inverse correlation between L. casei et rel.
and IgE level we observed in our study, caution must be taken in considering these data since only a low number of children were analyzed.
Characterized by a decrease of the absolute levels of Clostridium
cluster IV, F. prausnitzii
and A. muciniphila
, as well as a corresponding increase in the relative abundance of Enterobacteriaceae
, the atopy-associated intestinal microbial community we described in this study is depleted in key immunomodulatory members of the human intestinal microbiota and possibly enriched in pro-inflammatory “pathobionts” [41
]. By the specific induction of T regs, members of the Clostridium
cluster IV have been demonstrated to be strategic for maintaining the immune homeostasis [42
]. Analogously, providing a vast range of anti-inflammatory effects, F. prausnitzii
has been considered as a crucial microorganism for gut homeostasis [43
]. Finally, A. muciniphila
is a common member of the human intestinal tract which has been recently associated with a protective/anti-inflammatory role in healthy gut [44
]. On the other hand, Enterobacteriaceae
have been reported to prosper in the context of a host-mediated inflammatory response [45
]. Capable to venture more deeply in the mucus layer and establish a close interaction with the epithelial surface, members of Enterobacteriaceae
concur in the induction of a pro-inflammatory response and further consolidate the host inflammatory status. Thus, similarly to the one characterized in IBD [43
], the atopy-associated microbiota can represent an inflammogenic microbial consortium which can contribute to the severity of the disease [7