Comparative portrayal of ocular surface microbe with and without dry eye

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


Needs review

Curated date: 2023/09/09

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Conjunctiva Conjunctivae,Conjunctivas,Tunica conjunctiva,Wall of conjunctival sac,Conjunctiva
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
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)
No antibiotics for 6 months prior to study entry

Lab analysis

Sequencing type
16S
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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

Needs review

Curated date: 2023/09/09

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 4

Description: Fig. 4. 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 ControlLinks
Bacteroidia
bacteroidetesbacteroidetes

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2023/09/09

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 4

Description: Fig. 4. 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 ControlLinks
Pseudomonas plecoglossicida
Pseudomonadaceae
Pseudomonas
Gammaproteobacteria
Pseudomonadota

Revision editor(s): Mary Bearkland

Experiment 2


Needs review

Curated date: 2023/09/09

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
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

Needs review

Curated date: 2023/09/09

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 6

Description: Fig. 6. 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 ControlLinks
Bacillus pumilus
Bacillaceae
Bacillales
Bacilli

Revision editor(s): Mary Bearkland

Signature 2

Needs review

Curated date: 2023/09/09

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 6

Description: Fig. 6. 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 ofthe LEfSe algorithm.

Abundance in Group 1: decreased abundance in MGD

NCBI Quality ControlLinks
Bacteroidales
ruminococcaceaeruminococcaceae
Eubacterium coprostanoligenes
Alloprevotella
Thermomonas

Revision editor(s): Mary Bearkland