Microbiome of the Ocular Surface in Healthy and Diseased Eyes in Nigerian Populations: A Metagenomic Investigation

The ocular surface microbiome plays an increasingly recognised role in maintaining ocular surface health and may be dysregulated in conditions including dry eye disease, blepharitis, conjunctivitis, and corneal infection. Yet the ocular surface microbiome has been characterised almost exclusively in European and East Asian populations, leaving African microbiome profiles entirely unmapped. This study conducts a metagenomic investigation of the ocular surface microbiome in healthy Nigerian eyes and those with common anterior segment disease, generating the first African reference dataset. A cross-sectional comparative study will be conducted at Lagos University Teaching Hospital and Aminu Kano Teaching Hospital. Conjunctival swabs will be collected from 150 healthy volunteers and 150 patients with anterior segment disease categories including dry eye, bacterial conjunctivitis, blepharitis, and corneal ulcer. DNA will be extracted and subjected to 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. Bioinformatics pipelines will identify microbiome composition, alpha and beta diversity metrics, and the presence of antimicrobial resistance genes. Comparative analysis will examine differences between healthy and diseased eyes, North versus South Nigeria cohorts, and urban versus rural participants. The ocular surface microbiome has been shown in Western populations to be dominated by Staphylococci, Streptococci, and Corynebacteria, with dysbiosis associated with disease states. How the Nigerian tropical environment, hygiene behaviours, antibiotic exposure history, and diet influence ocular microbiome composition is unknown. This study generates foundational data for African ocular microbiome science. Recommendations will address integration of microbiome-based diagnostics into future ophthalmic infectious disease research in Nigeria and collaboration with the Human Heredity and Health in Africa consortium. Keywords: ocular surface microbiome, metagenomics, 16S rRNA sequencing, anterior segment, Nigeria