3.3 Fungal microbiome: community analysis
Ten samples out of 22 (45,4%) from VKC patients produced a detectable ITS2 amplicon and were sequenced. A total of 677,115 high-quality reads (average of 48,365 reads per sample) were clustered into 933 OTUs and taxonomically classified against the UNITE ver. 7.0 database. As for the 16S rRNA samples, rarefaction curves tended to saturation indicating that that the sequencing depth was reasonable (Figure 5S).
Alpha diversity metrics of fungal community didn’t substantially differ between HC and VKC children. However, Shannon index was significantly higher in IgE-negative than IgE-positive VKC patients (p=0.02), whereas the observed number of OTUs was significantly higher in males compared to females (p=0.01) (Figure 6S). Representing the microbiomes composition and structure through the PCoA plot, two distinct clusters emerged when comparing conjunctival microbiomes from VKC and HC samples as wells as from IgE-positive and IgE-negative subjects (Figure 7S).