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Thuy Doan, Lakshmi Akileswaran, Dallin Andersen, Narae Ko, Angira Shrestha, Cecilia S Lee, Aaron Lee, Russell Van Gelder; Human Ocular Surface Microbiome Composition Revealed By Next-Generation Sequencing. Invest. Ophthalmol. Vis. Sci. 2015;56(7 ):4067.
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© ARVO (1962-2015); The Authors (2016-present)
Human mucosal surfaces are thought to be colonized by a diverse community of microorganisms that help shape the immune system and when altered may lead to infections or cause inflammation in the host. Conventional culture techniques have failed to identify the composition and to characterize the diversity of these communities because a majority of these microbes are unculturable. In this study, we sought to characterize the ocular surface bacterial community in healthy subjects by using 16S rRNA gene deep sequencing on the Illumina platform.
Conjunctiva samples of the upper and lower fornices of both eyes were collected using forensic DNA recovery swabs from 35 healthy volunteers. Along with appropriate negative control samples, the conjunctiva samples underwent DNA extraction, library preparation, and 16S rRNA gene deep sequencing on the Illumina platform. Quantitative PCR for Torque Teno Virus (TTV) was also performed. Data were analyzed in R.
Sequencing resolution to the genus and species levels were obtained for 140 conjunctiva samples from 35 healthy volunteers. Propionibacterium acnes, Arthrospira fusiformis, Corynebacterium tuberculostearicum, Enterobacter hormaechei, and Chryseobacterium indologenes were the most abundant species across all samples. Principal component analyses showed that the genera responsible for the majority of the variance across all conjunctiva samples were Corynebacterium, Propionibacterium, and Staphylococcus. TTV was detected in 63% of the patients (17/27). Subgroup analyses revealed that the TTV load was statistically higher in men compared to women (0.012 TTV copy/epithelial cell ± 0.0028 TTV copy/epithelial cell vs. 0.001 TTV copy/epithelial cell ± 0.0006 TTV copy/epithelial cell, mean ± SEM, p = 0.0078).
The ocular surface microbiome bacterial composition in healthy volunteers is diverse. The variability across samples is largely determined by Corynebacterium, Propionibacterium, and Staphylococcus. Low TTV levels are found in the majority of the samples and TTV viral load is dependent on gender. Future experiments using unbiased next-generation sequencing to characterize the bacterial, fungal, and viral composition of the ocular surface will further our understanding of ocular infectious and inflammatory diseases.
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