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

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


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

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,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)
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 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

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

NCBI Quality ControlLinks
Deinococcus sp. NW-56
Pseudomonas aeruginosa

Revision editor(s): Mary Bearkland, ChiomaBlessing

Experiment 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

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

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

NCBI Quality ControlLinks
Pseudomonas aeruginosa
Malassezia globosa

Revision editor(s): Mary Bearkland, ChiomaBlessing

Experiment 3


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

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,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
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

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

Curated date: 2023/10/14

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

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

NCBI Quality ControlLinks
Staphylococcus aureus
Staphylococcus capitis

Revision editor(s): Mary Bearkland, ChiomaBlessing

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

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

NCBI Quality ControlLinks
Staphylococcus hominis

Revision editor(s): Mary Bearkland, ChiomaBlessing

Experiment 4


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

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

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

Curated date: 2023/10/15

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

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

NCBI Quality ControlLinks
Staphylococcus aureus
Staphylococcus capitis
Staphylococcus cohnii

Revision editor(s): Mary Bearkland, ChiomaBlessing

Experiment 5


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

Curated date: 2023/10/15

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, 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


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

Curated date: 2023/12/03

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

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

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

NCBI Quality ControlLinks
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

Experiment 7


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

Curated date: 2023/12/29

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
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

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

NCBI Quality ControlLinks
Janibacter melonis

Revision editor(s): Mary Bearkland

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

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

NCBI Quality ControlLinks
Capnocytophaga gingivalis

Revision editor(s): Mary Bearkland

Experiment 8


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

Curated date: 2023/12/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Folakunmi

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

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

Curated date: 2023/12/29

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

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

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

Revision editor(s): Mary Bearkland

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

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

NCBI Quality ControlLinks
Collinsella aerofaciens

Revision editor(s): Mary Bearkland