Morandi Sophia C, Uldry Anne-Christine, Eldridge Nina, Kreuzer Marco, Herzog Elio L, Zinkernagel Martin, Zysset-Burri Denise C
Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland.
Invest Ophthalmol Vis Sci. 2025 Jul 1;66(9):40. doi: 10.1167/iovs.66.9.40.
The field of ocular surface microbiome (OSM) research suggests its involvement in ocular surface (OS) health and disease. However, existing OSM data are heterogeneous. This study aims to provide a whole-metagenome shotgun sequencing-based description of the healthy core ocular surface microbiome (COSM), encompassing all taxonomic kingdoms at species-level resolution.
Swabs from the conjunctiva and lower lid margin, and tear fluid of 27 individuals without OS disease aged 40 to 60 years were collected at 3 time points. The OSM was sequenced and taxonomically and functionally profiled using Kraken2 and HUMAnN3, respectively. To validate sequencing results, human and microbial proteins of the tear fluid, termed the tear proteome (TP), were characterized by nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and profiled by gene ontology. The COSM was defined as the microbiome present in most of the study population over time. Therefore, species present in > 50% of all samples across the three time points were considered to form the COSM.
At species level, Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis formed the COSM, with Corynebacterium segmentosum additionally being part of the core lid microbiome (LM). No significant differences in the OSM and human TP were observed between the left and right eyes on individual levels. However, the variance between subjects mostly exceeded that between eyes within subjects, suggesting an individual-specific COSM and TP.
The description of the COSM provides the basis for future OSM research and potential targets for preventive and therapeutic interventions of the OS and associated diseases.
眼表微生物组（OSM）研究领域表明其与眼表（OS）健康及疾病有关。然而，现有的OSM数据具有异质性。本研究旨在提供基于全基因组鸟枪法测序的健康核心眼表微生物组（COSM）描述，在物种水平分辨率下涵盖所有分类界。
在3个时间点收集了27名年龄在40至60岁、无OS疾病个体的结膜、下睑缘拭子及泪液。分别使用Kraken2和HUMAnN3对OSM进行测序，并进行分类学和功能分析。为验证测序结果，通过纳升液相色谱-串联质谱（nLC-MS/MS）对泪液中的人类和微生物蛋白（即泪液蛋白质组，TP）进行表征，并通过基因本体进行分析。COSM被定义为在大多数研究人群中随时间存在的微生物组。因此，在三个时间点所有样本中出现率>50%的物种被认为构成COSM。
在物种水平上，痤疮丙酸杆菌、限制马拉色菌和表皮葡萄球菌构成了COSM，节段棒状杆菌 additionally 是核心睑微生物组（LM）的一部分。在个体水平上，左右眼之间的OSM和人类TP未观察到显著差异。然而，个体间的差异大多超过个体内双眼间的差异，提示存在个体特异性的COSM和TP。
COSM的描述为未来的OSM研究以及OS及相关疾病的预防和治疗干预的潜在靶点提供了基础。
