The closed eye harbours a unique microbiome in dry eye disease

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

32694705

DOI Digital object identifier for electronic documents.

10.1038/s41598-020-68952-w

URI

Authors

Willis KA, Postnikoff CK, Freeman A, Rezonzew G, Nichols K, Gaggar A, Lal CV

Journal

Scientific reports

Year

2020

Dry eye affects millions of individuals. In experimental models, dry eye disease is associated with T helper cell 17-mediated inflammation of the ocular surface that may cause persistent damage to the corneal epithelium. However, the initiating and perpetuating factors associated with chronic inflammation of the ocular surface remain unclear. The ocular microbiota alters ocular surface inflammation and may influence dry eye disease development and progression. Here, we collected serial samples of tears on awakening from sleep, closed eye tears, during a randomized clinical trial of a non-pharmaceutical dry eye therapy and used 16S rRNA metabarcoding to characterize the microbiome. We show the closed dry eye microbiome is distinct from the healthy closed eye microbiome, and that the microbiome remains distinct despite daily saline eye wash upon awakening. The ocular microbiome was described only recently, and this report implicates a distinct microbiome in ocular disease development. Our findings suggest an interplay between microbial commensals and inflammation on the ocular surface. This information may inform future studies of the pathophysiological mechanisms of dry eye disease.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14

Curated date: 2023/12/01

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy

Subjects

Location of subjects: United States of America

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: Tear film Precorneal film,Tear film,tear film

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: Normal Control (NC)

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: Participants with moderate or severe dry eye disease

Group 0 sample size Number of subjects in the control (unexposed) group: 36

Group 1 sample size Number of subjects in the case (exposed) group: 36

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Within 1 month was exclusionary

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: 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

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

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

Richness Number of species: unchanged

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14

Curated date: 2024/02/14

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Fig. S5 and Fig. S6.

Description: The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe).

Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).

Abundance in Group 1: increased abundance in Dry Eye

NCBI	Quality Control	Links
unclassified Lactobacillaceae
Streptococcus
Calothrix
Varibaculum
Rothia
Haemophilus
Meiothermus
Dialister
Dermacoccus
Prevotella
Faecalibacterium
Agrobacterium

Revision editor(s): Peace Sandy

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-14

Curated date: 2024/02/14

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source:

Description: The acquisition of unique taxa separates the dry from the normal eye at baseline. (b) Linear discriminant analysis of effect size (LEfSe).

Additional unique taxa separate the dry from the normal eye after a month. (b) Linear discriminant analysis of effect size (LEfSe).

Abundance in Group 1: decreased abundance in Dry Eye

NCBI	Quality Control	Links
Pseudomonas
unclassified Methylobacteriaceae
Helicobacter
Acetobacter
Bradyrhizobium
Stenotrophomonas
unclassified Coriobacteriaceae
Dietzia
Vogesella
Azospirillum
Pleomorphomonas
Peredibacter
unclassified Beijerinckiaceae
Rubellimicrobium
Escherichia
Rheinheimera

Revision editor(s): Peace Sandy