DNA extraction protocol impacts ocular surface microbiome profile

Heleen Delbeke; Ingele Casteels; Marie Joossens

doi:10.3389/fmicb.2023.1128917

DNA extraction protocol impacts ocular surface microbiome profile

Front Microbiol. 2023 Apr 20:14:1128917. doi: 10.3389/fmicb.2023.1128917. eCollection 2023.

Authors

Heleen Delbeke^{1

2}, Ingele Casteels^{1

2}, Marie Joossens³

Affiliations

¹ Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium.
² Department of Neurosciences, Research Group Ophthalmology, Biomedical Sciences Group, KU Leuven, Leuven, Belgium.
³ Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, Ghent, Belgium.

Abstract

Purpose: The aim of this study is to provide a reference frame to allow the comparison and interpretation of currently published studies on 16S ribosomal ribonucleic acid amplicon sequencing of ocular microbiome samples using different DNA extraction protocols. Alongside, the quantitative and qualitative yield and the reproducibility of different protocols has been assessed.

Methods: Both eyes of 7 eligible volunteers were sampled. Five commercially available DNA extraction protocols were selected based on previous publications in the field of the ocular surface microbiome and 2 host DNA depletion protocols were added based on their reported effective host DNA depletion without significant reduction in bacterial DNA concentration. The V3-V4 region of the 16S rRNA gene was targeted using Illumina MiSeq sequencing. The DADA2 pipeline in R was used to perform the bio-informatic processing and taxonomical assignment was done using the SILVA v132 database. The Vegdist function was used to calculate Bray-Curtis distances and the Galaxy web application was used to identify potential metagenomic biomarkers via linear discriminant analysis Effect Size (LEfSe). The R package Decontam was applied to control for potential contaminants.

Results: Samples analysed with PowerSoil, RNeasy and NucleoSpin had the highest DNA yield. The host DNA depletion kits showed a very low microbial DNA yield; and these samples were pooled per kit before sequencing. Despite pooling, 1 of both failed to construct a library.Looking at the beta-diversity, clear microbial compositional differences - dependent on the extraction protocol used - were observed and remained present after decontamination. Eighteen genera were consistently retrieved from the ocular surface of every volunteer by all non-pooled extraction kits and a comprehensive list of differentially abundant bacteria per extraction method was generated using LefSe analysis.

Conclusion: High-quality papers have been published in the field of the ocular surface microbiome but consensus on the importance of the extraction protocol used are lacking. Potential contaminants and discriminative genera per extraction protocol used, were introduced and a reference frame was built to facilitate both the interpretation of currently published papers and to ease future choice - making based on the research question at hand.

Keywords: 16SrRNA sequencing; DNA extraction protocol; eye microbiome; ocular surface microbiome; sequencing results.