*3.1. No Significant Differences in Alpha Diversity Indices*

No significant differences in diversity (Shannon's H'), species richness (observed number of OTUs) and evenness (Shannon's E) were found between controls and the participants with either AD, ADFA or FA, regardless of the compartment (skin and gut). Similarly, no differences were found between the group of allergic patients and those

without an allergy. However, the diversity of skin microbiota tended to be lower in AD patients (Figure 2). No correlations of any alpha-diversity indices were observed between the skin and feces, regardless of the analyzed group. Similarly, no differences were found between the group of allergic patients and those without an allergy. However, the diversity of skin microbiota tended to be lower in AD patients (Figure 2). No correlations of any alpha-diversity indices were observed between the skin and feces, regardless of the analyzed group.

No significant differences in diversity (Shannon's H'), species richness (observed number of OTUs) and evenness (Shannon's E) were found between controls and the participants with either AD, ADFA or FA, regardless of the compartment (skin and gut).

*Nutrients* **2021**, *13*, x FOR PEER REVIEW 8 of 20

*3.1. No Significant Differences in Alpha Diversity Indices* 

**3. Results** 

**Figure 2.** α-diversity of feces and skin microbiota in infants with FA, AD and ADFA. F—feces, S—skin, FA—food allergy, AD—atopic dermatitis, ADFA—atopis dermatitis and food allergy, C—control group. Panel A—Shannon's diversity index (H'), panel B—observed number of OTUs, panel C—Shannon's evenness (E). **Figure 2.** α-diversity of feces and skin microbiota in infants with FA, AD and ADFA. F—feces, S—skin, FA—food allergy, AD—atopic dermatitis, ADFA—atopis dermatitis and food allergy, C—control group. (**A**) Shannon's diversity index (H'), (**B**) Observed number of OTUs, (**C**) Shannon's evenness (E).

### *3.2. Gut and skin Microbiota Differ according to Clinical Status 3.2. Gut and Skin Microbiota Differ According to Clinical Status*

Significant differences were observed between the control, AD, ADFA and FA groups regarding fecal sample community structure (unweighted UniFrac distance, dbRDA, *p* = 0.003; Figure 3A). In addition, differences were found between ADFA and FA (*p* = 0.04) and between ADFA and control (*p* = 0.05).

(*p* = 0.04) and between ADFA and control (*p* = 0.05).

(Figure 3B).

**Figure 3.** (**A**,**B**). β-diversity of fecal and skin microbiota in the studied groups. β-diversity: distance based redundancy analysis (db RDA) on unweighted distance metrices calculated on rarified community data for: A—feces, B—skin, 95 % confidence elapses for show significance of grouping according to clinical status was tested FA—food allergy group, AD atopic dermatitis group, ADFA—atopic dermatitis and food allergy group, C—control group. **Figure 3.** (**A**,**B**). β-diversity of fecal and skin microbiota in the studied groups. β-diversity: distance based redundancy analysis (db RDA) on unweighted distance metrices calculated on rarified community data for: A—feces, B—skin, 95% confidence elapses for show significance of grouping according to clinical status was tested FA—food allergy group, AD—atopic dermatitis group, ADFA—atopic dermatitis and food allergy group, C—control group.

*3.3. There are Taxa Characteristic for Compartments and Clinical Status*  Any taxa whose abundance differed significantly between groups were regarded as characteristic for the group where the given taxon was more highly represented (Figure 4). Although no significant overall differences in skin communities were observed between groups (*p* = 0.15), significant differences became apparent when age (treated as continuous variable) was added to the overall model (*p* = 0.013). Regarding individual group comparisons, significant differences in the skin microbiome were found between AD and FA (*p* = 0.014), AD and control (*p* = 0.01), as well as AD and ADFA (*p* = 0.02) (Figure 3B).

Significant differences were observed between the control, AD, ADFA and FA groups regarding fecal sample community structure (unweighted UniFrac distance, dbRDA, *p* = 0.003; Figure 3A). In addition, differences were found between ADFA and FA

Although no significant overall differences in skin communities were observed between groups (*p* = 0.15), significant differences became apparent when age (treated as continuous variable) was added to the overall model (*p* = 0.013). Regarding individual group comparisons, significant differences in the skin microbiome were found between AD and FA (*p* = 0.014), AD and control (*p* = 0.01), as well as AD and ADFA (*p* = 0.02)
