Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children

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Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ju Zhang, Xiuhai Lu, Zhiwei Cheng, Dulei Zou
Journal
BMC microbiology
Year
2023
Pages:
11
First page:
397
Keywords:
Orthokeratology lenses, Conjunctiva sac, Microbiome, Microbiome, Brevundimonas, Acinetobacter, Proteus, genomics, 16s rdna gene sequencing
Background

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


Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26

Curated date: 2024/03/08

Curator: Ebere

Revision editor(s): Ebere, Peace Sandy

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

Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26

Curated date: 2024/03/08

Curator: Ebere

Revision editor(s): Ebere, Peace Sandy

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

NCBI Quality ControlLinks
Alphaproteobacteria
Caulobacteraceae
Caulobacterales
Brevundimonas
Actinomycetota
Bacilli
Sphingomonadales
Sphingomonadaceae
Corynebacteriaceae
Mycobacteriales
Moraxellaceae
Acinetobacter
Bacillales
Staphylococcaceae
unclassified Proteus (in: enterobacteria)
Enterobacterales
Micrococcales
Staphylococcus
Proteus
Cyanobacteriota
Xanthomonadaceae
Streptococcaceae
unclassified Corynebacterium
Streptococcus
Corynebacterium
Acidobacteriota
Planctomyces sp. SH-PL62
Enterococcaceae
Micrococcaceae
unclassified Enterobacter
Enterococcus
Chitinophagales
Propionibacteriales
Enterobacter
Flavobacteriales
Chitinophagaceae
Blautia
Bacillaceae
Propionibacteriaceae
Cutibacterium
Chloroflexia

Revision editor(s): Ebere, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26

Curated date: 2024/03/08

Curator: Ebere

Revision editor(s): Ebere, Peace Sandy

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 ControlLinks
Bacillus
Patescibacteria group
Akkermansia sp.
Muribaculaceae
unclassified Muribaculaceae

Revision editor(s): Ebere, Peace Sandy