Challenges and insights in the exploration of the low abundance human ocular surface microbiome.

Autor:	Herzog EL; Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.; Department for BioMedical Research, University of Bern, Bern, Switzerland.; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland., Kreuzer M; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland., Zinkernagel MS; Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.; Department for BioMedical Research, University of Bern, Bern, Switzerland., Zysset-Burri DC; Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.; Department for BioMedical Research, University of Bern, Bern, Switzerland.
Jazyk:	angličtina
Zdroj:	Frontiers in cellular and infection microbiology [Front Cell Infect Microbiol] 2023 Sep 01; Vol. 13, pp. 1232147. Date of Electronic Publication: 2023 Sep 01 (Print Publication: 2023).
DOI:	10.3389/fcimb.2023.1232147
Abstrakt:	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 Actinobacteria , Firmicutes and Proteobacteria . Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied. 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. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2023 Herzog, Kreuzer, Zinkernagel and Zysset-Burri.)
Databáze:	MEDLINE
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