Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye

Study information

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

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

37803284

DOI Digital object identifier for electronic documents.

10.1186/s12866-023-03013-6

URI

Authors

Chen Z, Xiao Y, Jia Y, Lin Q, Qian Y, Cui L, Xiang Z, Li M, Yang C, Zou H

Journal

BMC microbiology

Year

2023

Keywords:

Children and adolescents, Diabetes mellitus, Dry eye, Metagenome, Microecology, Ocular surface

BACKGROUND: Microbiome changes on the ocular surface may cause dry eyes. A metagenome assay was used to compare the microbiome composition and function of the ocular surface between diabetic children and adolescents with dry eye, diabetic children and adolescents without dry eye, and normal children. MATERIALS AND METHODS: Twenty children and adolescents aged 8 to 16 with diabetes were selected from the Shanghai Children and Adolescent Diabetes Eye Study. Ten healthy children and adolescents belonging to the same age group were selected from the outpatient clinic during the same period. The participants were classified into the dry eye group (DM-DE group, n = 10), the non-dry eye group (DM-NDE group, n = 10) and the normal group (NDM group, n = 10). A conjunctival sac swab was collected for metagenomic sequencing, and the relationship between the microbiome composition and functional gene differences on the ocular surface with dry eye was studied. RESULTS: The classification composition and metabolic function of the microorganisms on the ocular surface of children in the 3 groups were analyzed. It was found that children's ocular microbiota was composed of bacteria, viruses and fungi. There were significant differences in α diversity and β diversity of microbial composition of ocular surface between DM-DE group and NDM group(P<0.05). There were significant differences in α and β diversity of metabolic pathways between the two groups(P<0.05). The functional pathways of ocular surface microorganisms in diabetic children with dry eyes were mainly derived from human disease, antibiotic resistance genes, carbohydrate, coenzyme and lipid transport and metabolism-related functional genes; In normal children, the functional pathways were mainly derived from replication, recombination, repair, signal transduction and defense-related functional genes. CONCLUSION: The DM-DE group have unique microbial composition and functional metabolic pathways. The dominant species and unique metabolic pathways of the ocular surface in the DM-DE group may be involved in the pathogenesis of dry eye in diabetic children.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2023/11/11

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

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: Conjunctival sac Conjunctiva serous sac,Subbrillar sac,Conjunctival sac,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: Normal healthy (NDM) children

Group 1 name Corresponds to the case (exposed) group for case-control studies: Diabetic children with Dry Eye Disease (DM-DE)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children aged 8-16 with Diabetes and Dry Eye 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: 10

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

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Matched on Factors on which subjects have been matched on in a case-control study: age, body mass index, sex

Alpha Diversity

Chao1 Abundance-based estimator of species richness: decreased

Richness Number of species: decreased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2023/11/11

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

Source: Figure 3g and Results within text (Page 7, Last 6 lines, Under subheading: Composition and difference analysis of the ocular microbiome)

Description: Fig 3g: Species composition with significant difference at the species level between the NDM and DM-DE groups (top 20)

Abundance in Group 1: decreased abundance in Diabetic children with Dry Eye Disease (DM-DE)

NCBI	Quality Control	Links
Mycobacteroides abscessus
Novosphingobium nitrogenifigens
Novosphingobium sp. Fuku2-ISO-50
Paenibacillus odorifer
Staphylococcus aureus
Streptococcus gordonii
Vibrio agarivorans

Revision editor(s): Mary Bearkland, ChiomaBlessing

Signature 2

Edit History Delete

Flag for review

Your review change was submitted

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

Curated date: 2023/11/11

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

Source: Figure 3g and Results within text (Page 7, Last 6 lines, Under subheading: Composition and difference analysis of the ocular microbiome)

Description: Figure 3g Species composition with significant difference at the species level between the NDM and DM-DE groups (top 20)

Abundance in Group 1: increased abundance in Diabetic children with Dry Eye Disease (DM-DE)

NCBI	Quality Control	Links
Cordyceps militaris
Enterobacter mori
Leuconostoc sp. DORA_2
Salmonella enterica
Vibrio vulnificus

Revision editor(s): Mary Bearkland, ChiomaBlessing

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-26

Curated date: 2023/11/18

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Statistical test: ANOSIM

Alpha Diversity

Chao1 Abundance-based estimator of species richness: decreased

Richness Number of species: decreased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-26

Curated date: 2023/11/18

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, ChiomaBlessing

Source: Text on page 5; Under subheading "Composition and difference analysis of the ocular microbiome"

Description: Composition and Differential analysis of the ocular microbiome between NDM and DM-DE groups

Abundance in Group 1: increased abundance in Diabetic children with Dry Eye Disease (DM-DE)

NCBI	Quality Control	Links
Actinomycetota
Apicomplexa
Ascomycota
Chlamydia trachomatis
Enterobacter
Escherichia coli
Leuconostoc sp. DORA_2
Mycobacterium leprae
Plasmodium ovale
Salmonella enterica
Vibrio