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

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

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

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, 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

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

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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

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 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

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

Signature 2

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 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

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

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

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

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

Curated date: 2023/10/15

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 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

Your review change was submittedDuplicate this Experiment Add a new Signature

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

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

Curated date: 2023/12/03

Curator: Mary Bearkland

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

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

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

Curated date: 2023/12/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, WikiWorks

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

Revision editor(s): Mary Bearkland, WikiWorks

Signature 2

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

Curated date: 2023/12/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, WikiWorks

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

Revision editor(s): Mary Bearkland, WikiWorks

Experiment 8