*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).

The members of the Xanthomonadales and Xanthomonadaceae were more abundant in the skin communities of all allergic (AD + ADFA + FA) patients, than in healthy children (*p* = 0.04 and *p* = 0.004, respectively); however, the reverse was true for the order Lactobacillales (*p* = 0.045), family Streptococcaceae (*p* = 0.045), genus *Streptococcus* (*p* = 0.044), and OTU13 belonging to genus *Bradyrhizobium* (*p* = 0.019).

In the gut of allergic children, the following taxa were more abundant: phylum Bacteroidetes (*p* = 0.03), class Bacteroidia (*p* = 0.03), order Bacteroidales (*p* = 0.046), family Bacteroidaceae (*p* = 0.043) and genus *Bacteroides* (*p* = 0.043). At the OTU level, OTU35, affiliated with *Parabacteroides*, and OTU21, belonging to *Bacteroides,* were more abundant in allergic children (*p* = 0.039 and *p* = 0.008, respectively), while OTU94 (*Fusicatenibacter saccharivorans*; *p* = 0.049), OTU68 (*Lactococcus lactis*; *p* = 0.035) and OTU30 (*Serratia marcescens*; *p* = 0.035) were more common in the control group.

Comparing all four groups allowed the identification of taxa specific for a particular clinical picture. The highest abundance of phylum Proteobacteria was found in skin samples of AD patients; lower levels were observed in ADFA and the lowest in the FA and control groups (*p* = 0.02). Sequences affiliated with Streptococcaceae were most frequent in libraries derived from skin samples of healthy children, but were absent from patients with skin symptoms (AD and ADFA; *p* = 0.04), the same applied to genus *Streptococcus*

(*p* = 0.039). At the OTU level, only low abundance sequences (less than 10 reads across all groups) were found to be characteristic of a particular clinical picture. *Nutrients* **2021**, *13*, x FOR PEER REVIEW 10 of 20

**Figure 4.** Taxonomic composition: (**A**). phyla level, (**B**). class level, (**C**) order level, (**D**). family level, (**E**). genus level in feces and skin microbiota of the studied children. F-FA—feces in food allergy group, F-AD—feces in atopic dermatitis group, F-ADFA—feces in atopic dermatitis and food allergy group, F-C—feces in control group, S-FA–skin in food allergy group, S-AD—skin in atopic dermatitis group, S-ADFA—skin in atopic dermatitis and food allergy group, S-C—skin in control group. **Figure 4.** Taxonomic composition: (**A**). phyla level, (**B**). class level, (**C**) order level, (**D**). family level, (**E**). genus level in feces and skin microbiota of the studied children. F-FA—feces in food allergy group, F-AD—feces in atopic dermatitis group, F-ADFA—feces in atopic dermatitis and food allergy group, F-C—feces in control group, S-FA–skin in food allergy group, S-AD—skin in atopic dermatitis group, S-ADFA—skin in atopic dermatitis and food allergy group, S-C—skin in control group.

The members of the Xanthomonadales and Xanthomonadaceae were more abundant in the skin communities of all allergic (AD + ADFA + FA) patients, than in healthy children (*p* = 0.04 and *p* = 0.004, respectively); however, the reverse was true for the order Lactobacillales (*p* = 0.045), family Streptococcaceae (*p* = 0.045), genus *Streptococcus* (*p* = 0.044), and OTU13 belonging to genus *Bradyrhizobium* (*p* = 0.019). In the feces samples, phylum Bacteroidetes was more abundant in AD children, less frequent in ADFA and absent from healthy controls (*p* = 0.043); the same was observed to orders Bacteroidales and Xanthomonadales (*p* = 0.038 and *p* = 0.03, respectively), families Xanthomonadaceae and Bacteroidaceae (*p* = 0.03 and *p* = 0.043, respectively) and genera *Stenotrophomonas* and *Bacteroides* (*p* = 0.03 and *p* = 0.041, respectively). In contrast, the

In the gut of allergic children, the following taxa were more abundant: phylum

abundance of genus *Enterobacter* was higher in children with no intestinal symptoms (AD and control) but lower in those with a food allergy (FA and ADFA; *p* = 0.009). Differences in OTU abundance (Table 3) were also observed.

**Table 3.** Differentially abundant OTUs.


*p*-value of Kruskal–Wallis test is given.

To identify the taxa potentially involved in AD and FA pathogenesis, the results for the control group were compared with those from all patients with symptoms either on the skin (AD + ADFA) or in the gut (FA + ADFA) (Table 4). Libraries derived from skin of AD + ADFA patients displayed higher levels of the members of the order Xanthomonadales (*p* = 0.029) and the families Xanthomonadaceae and Corynebacteriaceae (*p* = 0.029 and *p* = 0.036, respectively). In addition, in the feces-derived libraries, class Bacteroidia (*p* = 0.007), order Bacteroidales (*p* = 0.004) and family Bacteroidaceae were found to be more common in AD + ADFA than in healthy children.

**Table 4.** Differentially represented OTUs—characteristic either for AD or FA.


*p*-value of Kruskal–Wallis test is given.

Libraries from the skin samples of children with FA (FA + ADFA) were more abundant in bacteria from the order Xanthomonadales (*p* = 0.016) and family Xanthomonadaceae (*p* = 0.016) than those from the feces samples. Differences at the OTU level were also observed: in the skin samples, OTU2 and OTU13 were more abundant among control patients than the AD and FA groups, respectively. In the feces samples, OTUs 11, 35 and 41 were more abundant in the AD group than controls, while only OTU21 was more abundant in FA patients than the controls (Table 4).
