Changes in the eye microbiota associated with contact lens wearing

Wearing contact lenses (CL) has been identified as a risk factor for the development of eye conditions such as giant papillary conjunctivitis and keratitis. We hypothesize that wearing contact lenses is associated with changes in the ocular microbiota. We compared the bacterial communities of the conjunctiva and skin under the eye from 58 subjects, and analyzed samples from 20 subjects (9 CL wearers and 11 non-CL wearers) taken at 3 time points using a 16S rRNA gene-based sequencing technique (V4 region, Illumina MiSeq). We found that using anesthetic eye drops before sampling decreases the detected ocular microbiota diversity. Compared to non-wearers, dry conjunctival swabs from CL-wearers had more variable and skin-like bacterial community structures (UniFrac; p-value <0.001), with higher abundance of Methylobacterium, Lactobacillus, Acinetobacter, and Pseudomonas and lower abundance of Haemophilus, Streptococcus, Staphylococcus, and Corynebacterium (LDA score >3.0). The results indicate that wearing contact lenses alters the microbial structure of the ocular conjunctiva, making it more similar to the skin microbiota. Further research is needed to determine whether the microbiome structure confers less resistance to ocular infections.