Comparative portrayal of ocular surface microbe with and without dry eye

Study information

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

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31463790

DOI Digital object identifier for electronic documents.

10.1007/s12275-019-9127-2

URI

Authors

Li Z, Gong Y, Chen S, Li S, Zhang Y, Zhong H, Wang Z, Chen Y, Deng Q, Jiang Y, Li L, Fu M, Yi G

Journal

Journal of microbiology (Seoul, Korea)

Year

2019

Keywords:

16S rRNA gene sequencing, dry eye, meibomian gland dysfunction, ocular surface bacteria

rRNA gene high-throughput sequencing was performed in the conjunctival swab samples to investigate the composition of the OS bacterial community in DE (n=35) and NDE (n=54) and compared the composition of MGD (n=25) and NMGD (n=10) among DE subjects. Deep sequencing of OS 16S rDNA from DE (n=35) and NDE (n=54) demonstrated great a difference in alpha and beta diversity between the OS bacterial flora (P < 0.05). The similar OS microbial structures were shown at the phylum and genus levels by bioinformatics analysis between them, and in LEfSe (linear discriminant analysis effect size) analysis, Bacteroidia and Bacteroidetes were enriched in DE, while Pseudomonas was plentiful in NDE (linear discriminant analysis [LDA] > 4.0). Among the DE group, there was no significant difference in α and β diversity between MGD and NMGD (P > 0.05). Surprisingly, Bacilli was the dominant microbe in MGD, and Bacteroidetes was the superior bacteria in NMGD among DE subjects (LDA > 4.0). Different diversity of OS bacteria composition between DE and NDE and the altered diversity of OS bacteria may play an important role in DE. Moreover, the lower dominance of OS bacteria in DE may be associated with the occurrence and development of DE. Although there was no significant difference in alpha and beta analysis, the OS dominant microbe between MGD and NMGD among DE was different.

Experiment 1

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

Curated date: 2023/09/09

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Peace Sandy, Folakunmi, KateRasheed

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

Conjunctiva Conjunctiva,conjunctiva,Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac

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

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 (with or without Meibomian Gland Disease). Subjects were considered to have DE if a positive dry eye survey OSDI ≥ 13 was recorded in addition to a positive score in one or more tests (tear break-up time ≤ 10; osmolarity ≥ 308 mOsm/L or interocular difference > 8 mOsm/L; ocular surface staining > 5 corneal spots, > 9 conjunctival spots, or lid margin ≥ 2 mm length, and 25% width).

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

35

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

6 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).

relative abundances

Statistical test

LEfSe

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

0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

4

Alpha Diversity

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

decreased

Chao1 Abundance-based estimator of species richness

unchanged

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

decreased

Richness Number of species

unchanged

Signature 1

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

Curated date: 2023/09/09

Curator: Mary Bearkland

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

Source: Figure 4

Description: Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the DE patients and NDE subjects as computed by the use of the LEfSe algorithm.

Abundance in Group 1: increased abundance in Dry Eye

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Bacteroidia

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

Signature 2

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

Curated date: 2023/09/09

Curator: Mary Bearkland

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

Source: Figure 4

Description: Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the DE patients and NDE subjects as computed by the use of the LEfSe algorithm.

Abundance in Group 1: increased abundance in Dry Eye

NCBI	Quality Control	Links
Gammaproteobacteria
Pseudomonadaceae
Pseudomonadota
Pseudomonas
Pseudomonas plecoglossicida

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: 2023/09/09

Curator: Mary Bearkland

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

Differences from previous experiment shown

Subjects

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

Non-MGD

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

MGD

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

Patients with Dry Eye with Meibomian Gland Disease

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

10

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

25

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

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

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

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

Curated date: 2023/09/09

Curator: Mary Bearkland

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

Source: Figure 6

Description: Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of the LEfSe algorithm.

Abundance in Group 1: increased abundance in MGD

NCBI	Quality Control	Links
Bacillaceae
Bacillales
Bacilli
Bacillus pumilus

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: 2023/09/09

Curator: Mary Bearkland

Revision editor(s): WikiWorks, Mary Bearkland, Aleru002, Folakunmi

Source: Figure 6

Description: Taxa listed according to their linear discriminant analysis (LDA) values determined from comparisons between the MGD patients and NMGD subjects in DE group as computed by the use of LEfSe algorithm.

Abundance in Group 1: decreased abundance in MGD

NCBI	Quality Control	Links
Alloprevotella
Bacteroidales
Eubacterium coprostanoligenes
Oscillospiraceae
Thermomonas

Revision editor(s): WikiWorks, Mary Bearkland, Aleru002, Folakunmi