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

Herzog, Elio L; Kreuzer, Marco; Zinkernagel, Martin S; Zysset-Burri, Denise C (2023). Challenges and insights in the exploration of the low abundance human ocular surface microbiome. Frontiers in cellular and infection microbiology, 13(1232147), p. 1232147. Frontiers 10.3389/fcimb.2023.1232147

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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.


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.


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.


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.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Department of Head Organs and Neurology (DKNS) > Clinic of Ophthalmology
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR)
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > Forschungsbereich Augenklinik > Forschungsgruppe Augenheilkunde
08 Faculty of Science > Department of Biology > Bioinformatics and Computational Biology

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Herzog, Elio Luca, Kreuzer, Marco Claudio, Zinkernagel, Martin Sebastian, Zysset, Denise Corinne


600 Technology > 610 Medicine & health








Pubmed Import

Date Deposited:

21 Sep 2023 15:26

Last Modified:

29 Oct 2023 02:23

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

DNA extraction kit host DNA depletion low abundance microbiome mechanical lysis nylon flocked swab ocular surface microbiome taxonomic profiling whole metagenome shotgun sequencing




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