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      Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome

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          Abstract

          Purpose

          To investigate the ocular surface microbiome of patients with unilateral or asymmetric glaucoma being treated with topical ophthalmic medications in one eye and to determine whether microbial community changes were related to measures of ocular surface disease.

          Methods

          V3-V4 16S rRNA sequencing was conducted on ocular surface swabs collected from both eyes of 17 subjects: 10 patients with asymmetric/unilateral glaucoma using topical glaucoma therapy on only one eye and seven age-matched, healthy controls with no history of ocular disease or eyedrop use. Samples were categorized into three groups: patients’ glaucomatous eye treated with eyedrops, patients’ contralateral eye without eyedrops, and healthy control eyes. Comparisons were made for microbial diversity and composition, with differences in composition tested for association with ocular surface disease measures including tear meniscus height, tear break-up time, and Dry Eye Questionnaire.

          Results

          Samples obtained from the patients’ treated and untreated eyes both had significantly greater alpha-diversity and relative abundance of gram-negative organisms compared to healthy controls. The microbial composition of patient eyes was associated with decreased tear meniscus height and tear break-up time, whereas metagenomic predictions, based on 16S rRNA data, suggested increased synthesis of lipopolysaccharide.

          Conclusions

          The ocular surface microbiome of patients taking unilateral preserved glaucoma drops is characterized by a highly diverse array of gram-negative bacteria that is significantly different from the predominantly gram-positive microbes detected on healthy control eyes. These compositional differences were associated with decreased tear film measures and distinct inferred protein synthesis pathways, suggesting a potential link between microbial alterations and ocular surface inflammation.

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          Most cited references70

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            DADA2: High resolution sample inference from Illumina amplicon data

            We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
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              The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

              SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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                Author and article information

                Journal
                Invest Ophthalmol Vis Sci
                Invest Ophthalmol Vis Sci
                IOVS
                Investigative Ophthalmology & Visual Science
                The Association for Research in Vision and Ophthalmology
                0146-0404
                1552-5783
                29 August 2022
                August 2022
                : 63
                : 9
                : 32
                Affiliations
                [1 ]Department of Ophthalmology, University of California San Francisco, San Francisco, California, United States
                [2 ]Department of Ophthalmology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
                [3 ]Department of Internal Medicine, Division of Infectious Disease, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
                [4 ]Department of Ophthalmology, New York University Langone Health, New York, New York, United States
                [5 ]Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California, United States
                [6 ]Ophthalmology Section, Surgical Service, San Francisco Veterans Affairs Medical Center, San Francisco, California, United States
                Author notes
                [* ]Correspondence: Bryan J. Winn, University of California San Francisco, 490 Illinois Street, 5th Floor, San Francisco, CA 94143, USA; bryan.winn@ 123456ucsf.edu.
                Article
                IOVS-22-35436
                10.1167/iovs.63.9.32
                9434984
                36036910
                1b26d0df-2909-4ab6-b65b-6e5e6e59969f
                Copyright 2022 The Authors

                This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

                History
                : 25 July 2022
                : 27 May 2022
                Page count
                Pages: 15
                Categories
                Immunology and Microbiology
                Immunology and Microbiology

                microbiome,ocular surface,preservatives,glaucoma medications,glaucoma

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