ArticleFrontiers in cellular and infection microbiology2023
Challenges and insights in the exploration of the low abundance human ocular surface microbiome.
Article in Frontiers in cellular and infection microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.Current opinion in ophthalmology · 2026Review
- From Health to Disease: A Comprehensive Review of Ocular Surface Microbiota and Detection Methods in Dry Eye.Current microbiology · 2026Review
- Uncovering the relationship between the human ocular surface microbiome and gut microbiome.BMC microbiology · 2026Article
- Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.Microbiology spectrum · 2026Article
- Linking the microbiome to the complement system in geographic atrophy.NPJ genomic medicine · 2026Article
- A Systematic Review of Bacterial Sampling Collection for Veterinary Microbiology in Companion Animals.Veterinary sciences · 2026Review
- Microbial modulation of proteoglycan and glycosaminoglycan biosynthesis in a three-dimensional corneal epithelium model.Frontiers in cellular and infection microbiology · 2026Article
- Metagenomic analysis of ocular microbiome in aqueous humor from myopia, cataract, primary open angle glaucoma and Posner-Schlossman syndrome.International journal of ophthalmology · 2026Article
- Crosstalk between gut microbiota and RNA N6-methyladenosine modification in diabetic retinopathy.Frontiers in cell and developmental biology · 2026Review
- The Ocular Surface Microbiome in Homeostasis and Dysbiosis.Microorganisms · 2025Review
- Toward the Characterization of the Human Core Ocular Surface Microbiome.Investigative ophthalmology & visual science · 2025Article
- Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.Journal of translational medicine · 2025Article
- Sequencing the ocular surface microbiome: a review of methodological practices and considerations.Frontiers in ophthalmology · 2025Review
- Exploring the Ocular Surface Microbiome and Tear Proteome in Glaucoma.International journal of molecular sciences · 2024Article
- Impact of Equine Ocular Surface Squamous Neoplasia on Interactions between Ocular Transcriptome and Microbiome.Veterinary sciences · 2024Article
- Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index.Biomolecules · 2024Article
- Altered ocular surface microbiota in obesity: a case-control study.Frontiers in cellular and infection microbiology · 2024Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Purpose: The low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes. Methods: Lower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2. Results: The total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Conclusion: The microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.
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