The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease

• Published in: International journal of molecular sciences Vol. 24; no. 18; p. 14091
• Main Authors: Schlegel, Irina, De Goüyon Matignon de Pontourade, Claire M. F., Lincke, Joel-Benjamin, Keller, Irene, Zinkernagel, Martin S., Zysset-Burri, Denise C.
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01-09-2023; MDPI
• Subjects: Analysis; Antibiotics; Antigens; Biosynthesis; Care and treatment; chromatography–tandem mass spectrometry; Classification; Drug resistance in microorganisms; dry eye disease; Eye diseases; Health care; Homeostasis; Lysine; Metadata; ocular surface microbiome; Pathogenesis; Physiological aspects; Proteins; Steroids; Taxonomy; tear proteome; whole-metagenome shotgun sequencing
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms241814091

Although dry eye disease (DED) is one of the most common ocular surface diseases worldwide, its pathogenesis is incompletely understood, and treatment options are limited. There is growing evidence that complex interactions between the ocular surface microbiome (OSM) and tear fluid constituents, potentially leading to inflammatory processes, are associated with ocular surface diseases such as DED. In this study, we aimed to find unique compositional and functional features of the OSM associated with human and microbial tear proteins in patients with DED. Applying whole-metagenome shotgun sequencing of forty lid and conjunctival swabs, we identified 229 taxa, with Actinobacteria and Proteobacteria being the most abundant phyla and Propionibacterium acnes the dominating species in the cohort. When DED patients were compared to controls, the species Corynebacterium tuberculostearicum was more abundant in conjunctival samples, whereas the family Propionibacteriaceae was more abundant in lid samples. Functional analysis showed that genes of L-lysine biosynthesis, tetrapyrrole biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis, and the super pathway of L-threonine biosynthesis were enriched in conjunctival samples of controls. The relative abundances of Acinetobacter johnsonii correlated with seven human tear proteins, including mucin-16. The three most abundant microbial tear proteins were the chaperone protein DnaK, the arsenical resistance protein ArsH, and helicase. Compositional and functional features of the OSM and the tear proteome are altered in patients with DED. Ultimately, this may help to design novel interventional therapeutics to target DED.