3.2 Bacterial microbiome: Taxonomic classification
The number of OTUs taxonomically assigned at the different levels are shown in the Supplementary File (Table 1S). At the phylum level, conjunctival microbiomes were dominated by Proteobacteria (VKC 44.8%; HC 67.9%), Firmicutes (VKC 37.0%; HC 22;1%), Actinobacteria (VKC 7.9%; HC 3.7%) and Bacteriodetes(VKC 4.2%; HC 2.7%) that accounted for > 90% of all the reads (Figure 3).
Proteobacteria, Firmicutes and Actinobacteria were present in all subjects qualifying theme as a putative core OS microbiome of both HC and VKC patients. In addition, Bacteroidetes andFusobacteria met the core microbiome’s definition criteria in VKC patients (Table 2), being present in > 80% of patients with a mean abundance > 0.01%. At the family level,Pseudomonadaceae (VKC 25.8%; HC 54.9%), Streptococcaceae(VKC 15.6%; HC 4.1%), Staphylococcaceae (VKC 12.5%; HC 9.5%), and Neisseriaceae (VKC 6.5%; HC 9.1%) were dominant in both groups (Figure 4S). Of the 132 observed families, Moraxellaceae(W=15) showed a higher abundance in VKC group than HC (Figure 4). At the genus level, 10 genera including Pseudomonas (VKC 25.7%; HC 54.8%), Staphylococcus (VKC 15.6%; HC 4.1%),Streptococcus (VKC 12.5%; HC 9.4%), Acinetobacter (VKC 5.5%; HC 0.1%), Neisseria (VKC 4.2%; HC 0.4%),Haemophilus (VKC 3.1%; HC 0.5%), Prevotella (VKC 1.1%; HC 1.1%), Corynebacterium (VKC 2.4%; HC 1.4%),Propionibacterium (VKC 2.0%; HC 0.1%) and Rothia (VKC 2.0%; HC 0.1%) accounted for > 70% of sequences in both groups (Figure 5).