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).