Impact of Contact Lenses and Pollen Allergies on the Ocular Surface Microbiome

Master's Thesis | Universities of Fribourg and Bern | August 2025
By Oriane Solange Kopp
Under supervision of Dr. phil. Denise Corinne Zysset-Burri, PhD

🔬 Abstract

This study investigates how contact lens wear and pollen allergies impact the ocular surface microbiome (OSM) and tear proteome using whole-metagenome shotgun sequencing (WMSS) and nano liquid chromatography tandem mass spectrometry (nLC-MS/MS).

Key Findings

• Contact Lenses: No significant differences in microbial composition or tear proteome between contact lens wearers and controls, though sex-specific responses and duration effects were observed
• Pollen Allergies: Significant association with Moraxella osloensis, representing a potential novel therapeutic target
• Methodology: Developed and validated decontamination methods for low-biomass microbiome studies

🎯 Study Objectives

1. Microbiome Analysis: Characterize OSM in contact lens wearers and pollen allergy sufferers vs. controls
2. Proteome Profiling: Analyze tear proteome differences between study populations
3. Clinical Assessment: Evaluate dry eye disease (DED) parameters and their relationship with OSM
4. Methodological Innovation: Implement decontamination methods for OSM contamination challenges

📊 Study Design

Cohorts

• Contact Lens Study: 25 wearers vs. 23 age-/sex-matched controls
• Pollen Allergy Study: 18 allergy sufferers vs. 21 age-/sex-matched controls

Methods

• Sequencing: Illumina NovaSeq 6000, 150bp paired-end reads
• Analysis Pipeline: MetaPhlAn4 for taxonomy, HUMAnN3 for function
• Proteomics: nLC-MS/MS with FragPipe/MSFragger processing
• Statistics: MaAsLin2, PERMANOVA, machine learning (Random Forest, SVM)

🧬 Key Results

Contact Lenses

• No significant overall differences in OSM composition or diversity
• Sex-stratified analysis revealed marginal differences in male participants
• Duration of wear showed significant association with OSM composition
• Increased subjective dry eye symptoms (OSDI©) in female contact lens wearers but otherwise no significant differences
• No differences in tear proteome composition
• Machine Learning models were not able to distinguish contact lens wearers from controls

Pollen Allergies

• Significant differences in OSM beta diversity (p = 0.007)
• Moraxella osloensis significantly more abundant in pollen allergy sufferers (q = 0.025)
• No differences in tear proteome composition

Methodological Contributions

• Novel decontamination approach: decontam + PubMed method
• Comparison of multiple contamination removal strategies

🔧 Technical Implementation

Decontamination Pipeline

Raw Data (from MetaPhlan4) → Decontam Analysis → Contextual Filtering (PubMed) → Clean Dataset

This method work by taking the list of species flagged as potential contaminant by decontam (based on the prevalence method) and perform a litteratur search to remove species from the contaminant list if those species are cited in at least 5 papers talking about the ocular surface.

Key Software & Packages

• Sequencing: UMI-tools, fastp, Bowtie2, SAMtools
• Microbiome: MetaPhlAn4, HUMAnN3, MaAsLin2, decontam
• Proteomics: FragPipe, MSFragger, IonQuant, DAVID bioinformatics
• Statistics: R (vegan, ggplot2, randomForest, e1071)

📁 Repository Structure

├── scripts/
│   ├── 1_decontamination_functions.R
│   ├── 2_analysis_functions.R
│   ├── 3_DED_score_functions.R
│   └── 4_protein_analysis.R
├── results/
│   └── ...

Those scripts are jsut snipnets of the scripts created during this project. Don't hesitate to contact me if you want to learn more.

🔬 Clinical Implications

Contact Lenses

• Well-adapted contact lens wearers may not show significant microbiome disruption
• Sex-specific responses warrant further investigation
• Duration effects suggest long-term monitoring may be beneficial

Pollen Allergies

• M. osloensis as potential therapeutic target
• Microbiome-based approaches for allergy treatment
• Novel diagnostic biomarker possibilities

⚠️ Limitations & Future Directions

Study Limitations

• Small sample sizes for subgroup analyses
• Low microbial biomass challenges

Future Research

• Larger longitudinal cohorts
• Investigation of M. osloensis therapeutic targeting
• Contact lens material and hygiene practice effects
• Seasonal variation in pollen allergy microbiome

📚 Publication

Publication currently under review

🙏 Acknowledgments

Special thanks to Dr. Denise C. Zysset-Burri for supervision, and the early project team including Sophia C. Morandi, Marco Kreuzer, and Anne-Christine Uldry.