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).