Ocular microbiome changes in dry eye disease and meibomian gland dysfunction

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-22
study design
prospective cohort
Citation
PMID PubMed identifier for scientific articles.
37586456
DOI Digital object identifier for electronic documents.
10.1016/j.exer.2023.109615
URI
Authors
Ozkan J, Majzoub ME, Coroneo M, Thomas T, Willcox M
Journal
Experimental eye research
Year
2023
Keywords:
16S rRNA gene sequencing, Dry eye disease, Meibomian gland dysfunction, Microbiome, Ocular microbiology
The most common and chronic ocular problem of aging is dry eye disease (DED) and the associated condition of meibomian gland dysfunction (MGD). The resident ocular surface bacteria may have a role in maintaining homeostasis and perturbation may contribute to disease development. The aim of this study was to compare the microbiomes of the conjunctiva and eyelid margin in humans with mild and moderate DED and controls using 16S rRNA gene sequencing. The conjunctiva and lid margin of three cohorts (N = 60; MGD, MGD with lacrimal dysfunction [MGD + LD] and controls) were swabbed bilaterally three times over three months. Microbial communities were analysed by extracting DNA and sequencing the V3-V4 region of the 16S ribosomal RNA gene using the Illumina MiSeq platform. Sequences were quality filtered, clustered into amplicon sequence variants (ASVs) using UNOISE algorithm and taxonomically classified using a Bayesian Last Common Ancestor (BCLA) algorithm against the GTDB 2207 database. The overall microbial communities of the MGD, MGD + LD and control groups were significantly different from each other (P = 0.001). The MGD and MGD + LD dry eye groups showed greater variability between individuals compared to the control (PERMDISP, P < 0.01). There was decreased richness and diversity in females compared to males for the conjunctiva (P < 0.04) and eyelid margin (P < 0.018). The conjunctiva in the MGD + LD group had more abundant Pseudomonas azotoformans, P. oleovorans and Caballeronia zhejiangensis compared to MGD and control (P < 0.05), while the MGD group had more abundant Corynebacterium macginleyi and C. kroppenstedtii compared to control (P < 0.05). The lid margin in MGD was more abundant in C. macginleyi, C. accolens, and C. simulans compared to the MGD + LD and control (P < 0.05). There were differences in the overall microbial community composition and certain taxa, including increased levels of lipophilic bacteria, on the conjunctiva and eyelid margin in mild to moderate DED/MGD compared to controls. DED/MGD was also associated with a reduced bacterial richness and diversity in females.

Experiment 1


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Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/22

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Folakunmi, Victoria

Subjects

Location of subjects
Australia
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
Margin of eyelid Free margin of eyelid,Margin of eyelid,margin of eyelid
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Dry eye syndrome dry eye,Dry Eye Syndrome,dry eye syndrome,Dry Eye Syndromes,dry eye(s),eye(s), dry,KCS,Keraconjunctivitis sicca,Keratoconjunctivitis Sicca,Keratoconjunctivitis sicca,keratoconjunctivitis sicca,Keratoconjunctivitis sicca (disorder),sicca, keratoconjunctivitis,Tear film insufficiency,tear film insufficiency,Dry eye syndrome
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Meibomian Gland Dysfunction
Group 1 name Corresponds to the case (exposed) group for case-control studies
Meibomian Gland Dysfunction + Lacrimal Dysfunction
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).
Group 0 sample size Number of subjects in the control (unexposed) group
15
Group 1 sample size Number of subjects in the case (exposed) group
17
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
No use of antibiotics in the prior 3 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).
raw counts
Statistical test
Linear Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/22

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 4

Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05

Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction

NCBI Quality ControlLinks
Pseudomonas putida   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Signature 2

EditHistoryDelete
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Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/22

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 4

Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05

Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction

NCBI Quality ControlLinks
Corynebacterium accolens   
Corynebacterium macginleyi   
Corynebacterium simulans   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Experiment 2


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Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/22

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Folakunmi, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy Control

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/22

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 4

Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05

Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction

NCBI Quality ControlLinks
Pseudomonas putida   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/22

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 4

Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups MGD+LD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05

Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction

NCBI Quality ControlLinks
Anaerococcus nagyae   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Experiment 3


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Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Folakunmi, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
Meibomian Gland Dysfunction
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with MGD corresponding to evaporative dry eye disease (moderate).
Group 1 sample size Number of subjects in the case (exposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 4

Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05

Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction

NCBI Quality ControlLinks
Corynebacterium accolens   
Corynebacterium macginleyi   
Corynebacterium simulans   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 4

Description: Bacteria identified at the eyelid margin which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate GLMs with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05

Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction

NCBI Quality ControlLinks
Anaerococcus nagyae   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Experiment 4


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Folakunmi, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Conjunctiva Conjunctiva,conjunctiva,Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Meibomian Gland Dysfunction
Group 1 name Corresponds to the case (exposed) group for case-control studies
Meibomian Gland Dysfunction + Lacrimal Dysfunction
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with MGD + LD corresponding to both evaporative dry eye disease and aqueous deficient dry eye disease (severe DED).
Group 1 sample size Number of subjects in the case (exposed) group
17

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 3

Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01

Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction

NCBI Quality ControlLinks
Caballeronia zhejiangensis   
Pseudomonas azotoformans   
Ectopseudomonas oleovorans   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 3

Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and MGD+LD. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01

Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction

NCBI Quality ControlLinks
Corynebacterium kroppenstedtii   
Corynebacterium macginleyi   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Experiment 5


EditHistoryDelete
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Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Folakunmi, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
control

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 3

Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups- MGD+LD and healthy controls. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01

Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction + Lacrimal Dysfunction

NCBI Quality ControlLinks
Caballeronia zhejiangensis   
Pseudomonas azotoformans   
Ectopseudomonas oleovorans   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Experiment 6


EditHistoryDelete
Flag for review
Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Folakunmi, Victoria

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Meibomian Gland Dysfunction
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants with MGD to evaporative dry eye disease (moderate DED).
Group 1 sample size Number of subjects in the case (exposed) group
15

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Folakunmi on 2023-12-22

Curated date: 2023/08/23

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

Source: Figure 3

Description: Bacteria identified from the conjunctiva which showed significant differences in mean relative abundance between the groups - MGD and healthy controls. Analysis conducted using univariate generalized linear models (GLMs) with negative binomial distribution. Data from male and female participants presented cumulatively. Error bars represent standard error of the mean. *P < 0.05, **P < 0.01

Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction

NCBI Quality ControlLinks
Corynebacterium kroppenstedtii   
Corynebacterium macginleyi   

Revision editor(s): Mary Bearkland, Folakunmi, WikiWorks

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