A Combined Analysis of Gut and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Study

Abstract

The gut microbiota in patients with food allergy, and the skin microbiota in atopic dermatitis patients differ from those of healthy people. We hypothesize that relationships may exist between gut and skin microbiota in patients with allergies. The aim of this study was to determine the possible relationship between gut and skin microbiota in patients with allergies, hence simultaneous analysis of the two compartments of microbiota was performed in infants with and without allergic symptoms. Fifty-nine infants with food allergy and/or atopic dermatitis and 28 healthy children were enrolled in the study. The skin and gut microbiota were evaluated using 16S rRNA gene amplicon sequencing. No significant differences in the α-diversity of dermal or fecal microbiota were observed between allergic and non-allergic infants; however, a significant relationship was found between bacterial community structure and allergy phenotypes, especially in the fecal samples. Certain clinical conditions were associated with characteristic bacterial taxa in the skin and gut microbiota. Positive correlations were found between skin and fecal samples in the abundance of Gemella among allergic infants, and Lactobacillus and Bacteroides among healthy infants. Although infants with allergies and healthy infants demonstrate microbiota with similar α-diversity, some differences in β-diversity and bacterial species abundance can be seen, which may depend on the phenotype of the allergy. For some organisms, their abundance in skin and feces samples may be correlated, and these correlations might serve as indicators of the host’s allergic state.

Mother’s Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis

“…The strengths and limitations of our study group were described earlier [28]. Additional strengths stem from the inclusion of milk; this is the first study analyzing the microbiomes of milk, skin and feces simultaneously.…”

“…The study group was described in detail earlier [28]. A diagram depicting the steps of patients' enrollment and the samples collected in this study is shown in Figure 1.…”

“…The methods of the fecal and skin samples collection were reported earlier [28]. Milk samples were taken during the enrollment visit with sterile, disposable equipment, and freshly expressed mothers' milk was gathered into collection tubes and frozen at −80 • C until further processing.…”

“…DNA was isolated and Illumina sequencing libraries generation was carried out as previously described [28,29]. The libraries were sequenced on MiSeq using 600 cycles v.3 kit (Illumina) at CMIT NCU.…”

“…The process of sequencing reads analysis was described earlier [28,29]. Briefly, it was performed in R with the use of functions from the dada2 package [30] and Silva v. 132 [31].…”