Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Orthokeratology (OK) lens wear increases the risk of bacterial infection, but little is known about the microbiota of the conjunctival sac in myopic children wearing OK lenses. This study aimed to investigate the changes of conjunctival microbiota in children after treatment with OK lenses using 16 S rDNA sequencing.
Methods Twenty-eight myopic children who had been continuously wearing OK lenses for 12 to 13 months were enrolled in this prospective study. Twenty-two gender- and age-matched myopic children who had not worn OK lenses or discontinued OK lens wear at least 1 year ago were recruited as controls. Conjunctival swabs from each participant were collected for exploration of the microbiota profiles, targeting the V3–V4 regions of the 16 S rRNA gene by MiSeq sequencing. The differences in the microbial community structure and diversity were also compared between groups.
Results The bacterial alpha diversity indices in the OK lens group were not different from those in the non-wearer group (P > 0.05, Wilcoxon test), while beta diversity examined using principle coordinate analysis of unweighted UniFrac divided the two groups into different clusters. Proteobacteria, Bacteroidetes, and Firmicutes were the abundant phyla in the conjunctival sac microbiota in both groups (P < 0.05, Mann–Whitney U test). Among children in the OK lens group, the Linear discriminant analysis Effect Size identified the compositional changes in OK lens-associated bacteria. Key functional genera such as Blautia, Parasutterella, and Muribaculum were enriched, whereas Brevundimonas, Acinetobacter, Proteus, and Agathobacter decreased significantly (P < 0.05, Mann–Whitney U test). Phylogenetic investigation of communities by reconstruction of unobserved states also showed altered bacterial metabolic pathways in OK lens-associated microbiota. Moreover, using receiver operating characteristic curves, Brevundimonas, Acinetobacter, Proteus, and Agathobacter alone (the area under the curve was all > 0.7500) or in combination (the area under the curve was 0.9058) were revealed to discriminate OK lens wearers from controls.
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Conjunctival sac Conjunctiva serous sac,Subbrillar sac,Conjunctival sac,conjunctival sac
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Myopia Close sighted,Near sighted,Near sightedness,Nearsightedness,Myopia,myopia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- N group - Non-wearer group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- L group - Ok Lens group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Myopic patients who had been wearing OK lenses for 12–13 months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig 4
Description: Linear Discriminant Analysis (LDA) Effect Size (LEfSe) multilevel discriminant analysis of the species differences (LDA > 3, P < 0.05, Mann–Whitney U-tests). A: Cladogram. The circle radiating from inside to outside represents the classification level from the kingdom to the genus (or species). Species with no significant differences are uniformly colored in yellow, the red nodes represent the microbial group that plays an important role in the OK group, and the green nodes represent the non-wearer group. B: Histogram of LDA value distribution shows the biomarkers with statistical difference. The LDA value represents the influence of bacterial species, and the longer the length, the higher the degree of influence. L: the OK lens group, N: the non-wearer group
Abundance in Group 1: increased abundance in L group - Ok Lens group
Revision editor(s): Ebere, Peace Sandy
Signature 2
Source: Fig 4
Description: Linear Discriminant Analysis (LDA) Effect Size (LEfSe) multilevel discriminant analysis of the species differences (LDA > 3, P < 0.05, Mann–Whitney U-tests). A: Cladogram. The circle radiating from inside to outside represents the classification level from the kingdom to the genus (or species). Species with no significant differences are uniformly colored in yellow, the red nodes represent the microbial group that plays an important role in the OK group, and the green nodes represent the non-wearer group. B: Histogram of LDA value distribution shows the biomarkers with statistical difference. The LDA value represents the influence of bacterial species, and the longer the length, the higher the degree of influence. L: the OK lens group, N: the non-wearer group
Abundance in Group 1: decreased abundance in L group - Ok Lens group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Patescibacteria group | ||
| Akkermansia sp. | ||
| Muribaculaceae | ||
| unclassified Muribaculaceae |
Revision editor(s): Ebere, Peace Sandy
