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

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

34900990

DOI Digital object identifier for electronic documents.

10.3389/fcell.2021.731867

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

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

Curated date: 2023/10/14

Curator: Mary Bearkland

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

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,bulbar conjunctiva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Biological sex 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)

3 months

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 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

Curated date: 2023/10/14

Curator: Mary Bearkland

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

Source: Supp fig 2c and 2d

Description: Sex-related differences of the conjunctival microbiota in patients with dry eye.

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

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Deinococcus sp. NW-56
Pseudomonas aeruginosa

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

Experiment 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, ChiomaBlessing, MyleeeA

Differences from previous experiment shown

Subjects

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

Healthy female

Group 1 name Corresponds to the case (exposed) group for case-control studies

Healthy male

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Healthy male without dry eye disease

Lab analysis

Statistical Analysis

Alpha Diversity

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

increased

Signature 1

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Source: Supp fig 2c and 2d, Figure 3D

Description: Sex-related differences of the conjunctival microbiota in healthy individuals.

Abundance in Group 1: increased abundance in Healthy male

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Pseudomonas aeruginosa
Malassezia globosa

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Experiment 3

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

Curated date: 2023/10/14

Curator: Mary Bearkland

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

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,Dry eye syndrome

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

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

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Curated date: 2023/10/14

Curator: Mary Bearkland

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Source: Supp. fig 5

Description: Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and meibomian gland dysfunction (MGD)

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

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Staphylococcus aureus
Staphylococcus capitis

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Signature 2

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Curated date: 2023/10/14

Curator: Mary Bearkland

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

Source: Supp. fig 5

Description: Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and meibomian gland dysfunction (MGD)

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

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Staphylococcus hominis

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Experiment 4

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

Curated date: 2023/10/14

Curator: Mary Bearkland

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

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

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Curated date: 2023/10/15

Curator: Mary Bearkland

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Source: Supp fig 5

Description: Differentially abundant Staphylococcus species between patients with aqueous tear deficiency (ATD) and mixed dry eye

Abundance in Group 1: increased abundance in Mixed DED

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Staphylococcus aureus
Staphylococcus capitis
Staphylococcus cohnii

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

Experiment 5

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

Curated date: 2023/10/15

Curator: Mary Bearkland

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

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

Alpha Diversity

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

unchanged

Experiment 6

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-23

Curated date: 2023/12/03

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, ChiomaBlessing, MyleeeA

Differences from previous experiment shown

Subjects

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

healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies

Dry Eye

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients with Dry eye disease

Group 0 sample size Number of subjects in the control (unexposed) group

48

Group 1 sample size Number of subjects in the case (exposed) group

47

Lab analysis

Statistical Analysis

Statistical test

MaAsLin2

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

decreased

Signature 1

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Source: Supp table 4

Description: Comparison between dry eye group and healthy group showing species with polarized abundance (decreased abundance) in dry eye samples

Abundance in Group 1: increased abundance in Dry Eye

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Acinetobacter radioresistens
Acinetobacter sp. WCHA45
Aggregatibacter segnis
Chryseobacterium sp.
Chryseobacterium taklimakanense
Corynebacterium matruchotii
Deinococcus ficus
Deinococcus sp. NW-56
Fusobacterium nucleatum
Janibacter melonis
Lactobacillus iners
Malassezia globosa
Micropruina glycogenica
Neisseria subflava
Paracoccus yeei
Parvimonas micra
Rothia mucilaginosa
Staphylococcus aureus
Staphylococcus hominis
Streptococcus sanguinis
Streptococcus sp. oral taxon 431
Veillonella parvula
unclassified Corynebacterium

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

Experiment 7

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-23

Curated date: 2023/12/29

Curator: Mary Bearkland

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

Differences from previous experiment shown

Subjects

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

Dry Eye -nonATD

Group 1 name Corresponds to the case (exposed) group for case-control studies

Dry Eye- ATD

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients with Dry eye disease characterized as aqueous tear deficient

Group 0 sample size Number of subjects in the control (unexposed) group

54

Group 1 sample size Number of subjects in the case (exposed) group

14

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.1

Signature 1

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Source: Figure 4b

Description: B) Model coefficients of top-ranked species associated with either ATD or non-ATD dry eye (p < 0.1, coefficient >0.2)

Abundance in Group 1: increased abundance in Dry Eye- ATD

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Janibacter melonis

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Signature 2

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Source: Figure 4b

Description: Figure 4b) Model coefficients of top-ranked species associated with either ATD or non-ATD dry eye (p < 0.1, coefficient >0.2) (

Abundance in Group 1: decreased abundance in Dry Eye- ATD

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Capnocytophaga gingivalis

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Experiment 8

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-23

Curated date: 2023/12/29

Curator: Mary Bearkland

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

Differences from previous experiment shown

Subjects

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

Dry Eye -nonMGD

Group 1 name Corresponds to the case (exposed) group for case-control studies

Dry Eye- MGD

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients with Dry eye disease characterized as meibomian gland disorder

Group 0 sample size Number of subjects in the control (unexposed) group

49

Group 1 sample size Number of subjects in the case (exposed) group

19

Lab analysis

Statistical Analysis

Signature 1

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Source: Figure 4c

Description: Model coefficients of top-ranked species associated with either MGD or non-MGD dry eye (p < 0.1, coefficient >0.2)

Abundance in Group 1: increased abundance in Dry Eye- MGD

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Acinetobacter sp. WCHA45
Deinococcus sp. NW-56
Staphylococcus aureus
Staphylococcus capitis
Staphylococcus cohnii

Revision editor(s): Mary Bearkland, WikiWorks

Signature 2

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Source: Figure 4c

Description: Model coefficients of top-ranked species associated with either MGD or non-MGD dry eye (p < 0.1, coefficient >0.2)

Abundance in Group 1: decreased abundance in Dry Eye- MGD

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Collinsella aerofaciens

Revision editor(s): Mary Bearkland, WikiWorks