Changes in the Eye Microbiota Associated with Contact Lens Wearing

Abstract

Wearing contact lenses has been identified as a risk factor for the development of eye conditions such as giant papillary conjunctivitis and keratitis. We hypothesized 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 lens wearers and 11 non-lens 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 those from non-lens wearers, dry conjunctival swabs from lens wearers had more variable and skin-like bacterial community structures (UniFrac;P value = <0.001), with higher abundances of Methylobacterium,Lactobacillus,Acinetobacter, andPseudomonasand lower abundances of Haemophilus,Streptococcus,Staphylococcus, and Corynebacterium(linear discriminant analysis [LDA] score = >3.0). The results indicate that wearing contact lenses alters the microbial structure of the ocular conjunctiva, making it more similar to that of the skin microbiota. Further research is needed to determine whether the microbiome structure provides less protection from ocular infections.

Importance: As in other body sites (i.e., the gut, skin, and mouth), the eye has a normal community of bacteria which are expected to confer resistance that provides protection from invaders. However, the eye microbiome has been largely neglected and is relevant to eye health and understanding eye diseases and to discovery of its functions. This report of a baseline study shows differences in the eye microbiome of contact lens wearers in relation to those of non-lens wearers and has the potential to help future studies explore novel insights into a possible role of the microbiome in the increased risk for eye infections in contact lens wearers.

FIG 1

Bacterial diversity in the conjunctiva, skin, and contact lens between non-lens wearers and lens wearers. Box plots of alpha diversity were generated with rarefication to 2,090 reads per sample. The nonparametric P values were calculated using 999 Monte Carlo permutations. +, outlier samples excluded from the analyses; **, P value = <0.05.

FIG 2

Beta diversity in conjunctiva, skin, and contact lens samples between non-lens wearers and lens wearers. Unweighted UniFrac distances were used to evaluate diversities between samples. (A) PCoA plot of bacterial communities by body site, time, and subject in non-lens wearers (left) and lens wearers (right). PC1, first principal component; PC2, second principal component. (B) Box plots of intragroup and intergroup distances in bacterial communities between conjunctiva and skin under the eye. (C) PCoA plot of ocular microbiota in non-lens wearers and lens wearers with bacterial communities of contact lenses. (D) Box plots of intragroup and intergroup distances in the ocular microbiota of non-lens wearers and lens wearers. ***, P value = <0.001.

FIG 3

Beta diversity in conjunctiva, skin, and contact lens samples with samples from the HMP database. A PCoA plot was generated using unweighted UniFrac distances. Small dots (green, purple, cyan, and pink) indicate samples from the HMP database, and large dots (red, orange, yellow, and blue) indicate samples from this study.

FIG 4

Differences in relative abundances of phylotypes in ocular microbiota between non-lens wearers and lens wearers. Each phylotype (>1% of average relative abundance in groups) is indicated by a different color at the genus level. (A) Bacterial taxon plots at the genus level. (B) Histogram of unique biomarker bacteria in each group. The LDA effect size (>3.0-fold) was used to detect unique biomarkers.