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Toward the Characterization of the Human Core Ocular Surface Microbiome
Sophia C Morandi1,2, Anne-Christine Uldry2, Nina Eldridge1
1Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
Investigative Ophthalmology & Visual Science
|July 14, 2025
Summary
This study defines the healthy core ocular surface microbiome (COSM) using whole-metagenome sequencing. Key species like Cutibacterium acnes and Staphylococcus epidermidis form the COSM, crucial for understanding ocular surface health and disease.
Area of Science:
- Microbiology
- Ophthalmology
- Metagenomics
Background:
- The ocular surface microbiome (OSM) plays a role in ocular surface (OS) health and disease.
- Current OSM data are inconsistent, necessitating a standardized description.
- Understanding the healthy OSM is vital for identifying disease-related alterations.
Purpose of the Study:
- To characterize the healthy core ocular surface microbiome (COSM) using whole-metagenome shotgun sequencing.
- To provide a species-level resolution of the OSM across all taxonomic kingdoms.
- To establish a baseline for future research into OSM and ocular surface diseases.
Main Methods:
- Collected conjunctival, lid margin, and tear fluid samples from 27 healthy individuals over 3 time points.
- Sequenced OSM using whole-metagenome shotgun sequencing and profiled with Kraken2 and HUMAnN3.
- Validated findings by characterizing the tear proteome (TP) using nLC-MS/MS and gene ontology.
Main Results:
- Identified Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis as core COSM species.
- Corynebacterium segmentosum was identified as part of the core lid microbiome (LM).
- Observed significant inter-individual variation in OSM and TP, exceeding intra-individual differences.
Conclusions:
- The defined COSM serves as a foundational reference for ocular surface microbiome research.
- This characterization may inform future preventive and therapeutic strategies for ocular surface diseases.
- Individual-specific microbiome signatures are a key feature of the ocular surface environment.
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