Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L, Wen X
Journal
Frontiers in cell and developmental biology
Year
2021
Keywords:
aqueous tear deficiency, conjunctival microbiota, dry eye disease, meibomian gland dysfunction, metagenomic shotgun sequencing
Background: Dry eye disease (DED) is a multifactorial inflammatory disease of the ocular surface. It is hypothesized that dysbiosis of the conjunctival microbiota contributes to the development of DED. However, species-level compositions of the conjunctival microbiota in DED and the potential dysbiosis involving microorganisms other than bacteria remain largely uncharacterized. Methods: We collected conjunctival impression samples from a cohort of 95 individuals, including 47 patients with DED and 48 healthy subjects. We examined the conjunctival microbiota of these samples using shotgun metagenomic sequencing and analyzed microbial dysbiosis in DED at the species level. Results: The conjunctival microbiota in DED exhibited a decreased α-diversity and an increased inter-individual variation. The α-diversity of female patients with DED was higher than that of male patients. Despite a decreased prevalence in DED, 23 microbial species were identified to show abnormally high abundance in DED samples positive for the species. Among these species, a fungal species Malassezia globosa was enriched female patients. In addition, distinct patterns of associations with disease status were observed for different species of the same genus. For DED subtypes, Staphylococcus aureus and S. capitis were associated with meibomian gland dysfunction (MGD), whereas S. hominis was enriched in patients solely with aqueous tear deficiency (ATD). The microbiota of patients with a mixed type of diagnosis was more similar to MGD patients than ATD patients. Conclusion: We demonstrated that the conjunctival microbiota dysbiosis in DED is characterized by significant heterogeneity. Microbial signatures may offer novel insights into the complicated etiology of DED and potentially promote the development of personalized treatment for DED in the future.

Experiment 1


Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

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
Bulbar conjunctiva Ocular conjunctiva,Bulbar conjunctiva
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
biological sex biological sex
Group 0 name Corresponds to the control (unexposed) group for case-control studies
female patients with dry eye disease
Group 1 name Corresponds to the case (exposed) group for case-control studies
male patients with dry eye disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
male patients with dry eye disease
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
25
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
90 days prior to enrollment

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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
Linear Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supplemental 2c and 2d

Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.

Abundance in Group 1: increased abundance in male patients with dry eye disease

NCBI Quality ControlLinks

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 2c and 2d

Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.

Abundance in Group 1: decreased abundance in male patients with dry eye disease

NCBI Quality ControlLinks
Pseudomonas aeruginosa
Deinococcus sp. NW-56

Revision editor(s): Mary Bearkland

Experiment 2


Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
female
Group 1 name Corresponds to the case (exposed) group for case-control studies
male
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
male

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased

Signature 1

Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 2c and 2d

Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.

Abundance in Group 1: increased abundance in male

NCBI Quality ControlLinks
Pseudomonas aeruginosa

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 2c and 2d

Description: Supplementary Figure 2. Sex-related differences of the conjunctival microbiota in healthy individuals and patients with dry eye. Sex-related differences in the relative abundance of Pseudomonas aeruginosa (C) and Deinococcus sp. NW-56 (D) in healthy individuals and patients with dry eye. P values were derived from multivariable regression adjusting for age.

Abundance in Group 1: decreased abundance in male

NCBI Quality ControlLinks

Revision editor(s): Mary Bearkland

Experiment 3


Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Aqueous tear deficient (ATD) DED
Group 1 name Corresponds to the case (exposed) group for case-control studies
Meibomian Gland Dysfunction (MGD) DED
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with MGD DED
Group 0 sample size Number of subjects in the control (unexposed) group
14
Group 1 sample size Number of subjects in the case (exposed) group
19
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
90 days prior to study enrollment

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.15
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 5

Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.

Abundance in Group 1: increased abundance in Meibomian Gland Dysfunction (MGD) DED

NCBI Quality ControlLinks
Staphylococcus capitis
Staphylococcus aureus

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 5

Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.

Abundance in Group 1: decreased abundance in Meibomian Gland Dysfunction (MGD) DED

NCBI Quality ControlLinks
Staphylococcus hominis

Revision editor(s): Mary Bearkland

Experiment 4


Needs review

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Mixed DED
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with mixed type diagnosis of DED (more closely related to MGD than ATD)
Group 1 sample size Number of subjects in the case (exposed) group
35

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased

Signature 1

Needs review

Curated date: 2023/10/15

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 5

Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.

Abundance in Group 1: increased abundance in Mixed DED

NCBI Quality ControlLinks
Staphylococcus capitis
Staphylococcus aureus
Staphylococcus cohnii

Revision editor(s): Mary Bearkland

Experiment 5


Needs review

Curated date: 2023/10/15

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Meibomian Gland Dysfunction (MGD) DED
Group 0 sample size Number of subjects in the control (unexposed) group
19

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged

Signature 1

Needs review

Curated date: 2023/10/15

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 5

Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.

Abundance in Group 1: increased abundance in Mixed DED

NCBI Quality ControlLinks

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2023/10/15

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Supp fig 5

Description: Supplementary Figure 5. Staphylococcus species showing differences in abundance among patients with aqueous tear deficiency (ATD), meibomian gland dysfunction (MGD), and mixed dry eye. The species that were present in at least 10% of the dry eye samples and differentially abundant (P < 0.15) among the three groups were shown. P values were computed using Wilcoxon’s rank sum test. Relative abundances are represented as mean ± SEM. Error bars indicate standard error.

Abundance in Group 1: decreased abundance in Mixed DED

NCBI Quality ControlLinks

Revision editor(s): Mary Bearkland