Geographic Difference Shaped Human Ocular Surface Metagenome of Young Han Chinese From Beijing, Wenzhou, and Guangzhou Cities

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-14

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

32106294

DOI Digital object identifier for electronic documents.

10.1167/iovs.61.2.47

URI

Authors

Deng Y, Wen X, Hu X, Zou Y, Zhao C, Chen X, Miao L, Li X, Deng X, Bible PW, Ke H, Situ J, Guo S, Liang J, Chen T, Zou B, Liu Y, Chen W, Wu K, Zhang M, Jin ZB, Liang L, Wei L

Journal

Investigative ophthalmology & visual science

Year

2020

PURPOSE: Microbial ecosystems interact with the human body and affect human health. The microbial community on the ocular surface remains an underexplored territory despite its importance as the first line of defense barrier that protects the eye and ultimately sight. We investigated how age and sex affected human ocular surface microbiome, and in the present study wanted to understand how geographic difference shaped the microbiome in the ocular surface. METHODS: We collected conjunctival specimens of 172 eyes from 86 healthy volunteers living in three Chinese cities, namely, Guangzhou, Wenzhou, and Beijing. Using the direct metagenomic shotgun sequencing approach, we characterized how geographic difference affected the human ocular microbiome. RESULTS: We surveyed the taxonomic composition and metabolic function of the microbiota on human ocular surface. We showed that the ocular surface microbiota was composed of bacteria, viruses, and fungi. A geographical difference in both composition and function of the conjunctival microbiome suggests that the environment people lived in shapes their conjunctival microbiome, especially the dominate species. CONCLUSIONS: Our study provides a reference catalog of the healthy conjunctival metagenome and raises a concern for environmental influences on the ocular surface microbiome.

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 2024-1-14

Curated date: 2023/10/01

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: Health study participation health questionnaire participation,health survey participation,Health study participation,health study participation

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Guangzhou healthy volunteers

Group 1 name Corresponds to the case (exposed) group for case-control studies: Bejing healthy volunteers

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

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: 20

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months 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: LEfSe

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3

Alpha Diversity

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

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-14

Curated date: 2023/10/01

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Peace Sandy

Source: Figure 4

Description: Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).

Abundance in Group 1: increased abundance in Bejing healthy volunteers

NCBI	Quality Control	Links
Bacillus cereus
Brucella anthropi
Cereibacter sphaeroides
Corynebacterium aurimucosum
Corynebacterium jeikeium
Corynebacterium urealyticum
Delftia acidovorans
Delftia sp.
Enterococcus faecalis
Escherichia coli
Gordonia polyisoprenivorans
Kytococcus sedentarius
Micrococcus luteus
Neisseria meningitidis
Porphyromonas gingivalis
Pseudomonas aeruginosa
Ralstonia pickettii
Rhizobium sp.

Revision editor(s): Mary Bearkland, Peace Sandy

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-14

Curated date: 2023/10/01

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland

Source: Figure 4

Description: Figure 4: The characteristics of Guangzhou and Beijing conjunctival microbiome (A). The LDA effect size program was used to find the bacterial species which significantly distinguished Beijing (green) and Guangzhou (red) microbiomes (LDA score >3).

Abundance in Group 1: decreased abundance in Bejing healthy volunteers

NCBI	Quality Control	Links
Listeria monocytogenes
Ectopseudomonas mendocina
Brachyspira murdochii
Candidatus Karelsulcia
Stenotrophomonas maltophilia
Mycoplasmopsis bovis
Acidovorax sp.
[Acidovorax] ebreus
Mesomycoplasma hyorhinis
Cutibacterium acnes

Revision editor(s): Mary Bearkland