Amplicon-Based Metagenomic Assessment of the Skin Microbiota in a Healthy Middle Eastern Cohort: The Lebanese Population

Abstract

Background: Skin microbiota is a complex ecosystem that plays an important role in immune system regulation, skin homeostasis and protection against pathogens. The composition of skin microbial communities is affected by recipient genetics, environmental factors, geography and lifestyle factors. Although the skin microbiota has lately been studied in many populations, studies on the Lebanese population remain limited, which has a distinct genetic and environmental variety.

Aim: This study seeks to characterize the cultivable/enrichment-biased skin microbiota of Lebanese individuals under controlled culture conditions. By identifying the prevalent bacterial taxa and patterns of diversity after pre-enrichment, this study provides an initial reference framework for future research into dermatological issues in the Lebanese population and the role of microbial dysbiosis in disease.

Methods: Forehead skin swabs were collected from fourteen healthy Lebanese individuals, with no known skin disorders. These samples were pre-enriched in aerobic hemoculture bottles at different temperatures due to the low microbial biomass of skin samples and insufficient DNA yield for direct sequencing. While this approach enabled successful amplification and sequencing, it may have introduced a selection bias favoring fast-growing and aerotolerant microorganisms. DNA was extracted and sequenced for 16S rRNA genes using the Illumina MiSeq platform. Bioinformatics tools were then used to determine taxonomic composition, and alpha diversity indices across the included samples.

Results: In this study, at the phylum level, Bacillota was detected across the enriched samples, whereas Actinomycetota and Pseudomonadota were detected in fewer samples. At the genus level, Staphylococcus was most consistently detected across samples, including common commensal species, while several environmental-associated taxa were also detected. In addition, alpha diversity indices showed variability in evenness, richness and dominance among the enriched samples.

Conclusion: This study helps to address an important regional knowledge gap in the Middle East, by providing an initial characterization of cultivable/enrichment-biased skin microbiota of Lebanese individuals. The results show marked inter-individual variability, as well as shared patterns across individuals. This study highlights the need for region-specific studies and may serve as a reference for future research studying skin disease such as atopic dermatitis (AD), psoriasis, and acne in Lebanon.