Distribution and Diversity of Ocular Microbial Communities in Diabetic Patients Compared with Healthy Subjects
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ham B, Hwang HB, Jung SH, Chang S, Kang KD, Kwon MJ
Journal
Current eye research
Year
2018
Keywords:
Bacterial diversity, Bradyrhizobiaceae, Burkholderia, LFR analysis, Staphylococcus
PURPOSE: The aim of this study was to identify differences in the major (core vs. variable) microbial genera of human subjects with and without diabetes. METHODS: Bacterial 16S rRNA genes obtained from conjunctival swabs of 19 healthy subjects and 30 diabetic patients were sequenced using the Illumina MiSeq platform, and the sequencing data were analyzed using QIIME 1.9.1. To elucidate the microbial diversity in the ocular surface (OS), test programs from various bioinformatics domains were used. RESULTS: Diversity index and rarefaction analysis showed that the microbial community of the diabetic patients was more diverse than that of the healthy subjects. Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria and Bacteroidetes were the dominant taxa present in the OS, and there was a significant difference in the relative abundance of the bacterial phyla between the diabetic patients and control subjects. Proteobacteria were more abundant in the diabetic group, whereas Firmicutes was more abundant in the control group. Analysis of bacterial taxa at the genus level showed that the core microbiome of diabetic patients comprised Acinetobacter, Burkholderia, Sphingomonas, and Ralstonia, whereas that of the controls comprised Bradyrhizobiaceae, Staphylococcus, Corynebacterium, Pseudomonas, Novosphingobium, Neisseriaceae, and Acinetobacter. CONCLUSIONS: There was a significant difference in the microbial community composition between diabetic patients and healthy subjects. A high abundance of Acinetobacter in the OS of diabetic patients may arise from the unique characteristics of the OS compared with those of other organ surfaces.
Experiment 1
Reviewed Marked as Reviewed by Peace Sandy on 2023-12-30
Subjects
- Location of subjects
- Republic of Korea
- 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
- Type II diabetes mellitus adult onset diabetes,Adult-Onset Diabetes,adult-onset diabetes,Adult-Onset Diabetes Mellitus,diabetes mellitis type 2,diabetes mellitis type II,DIABETES MELLITUS TYPE 02,diabetes mellitus type 2,Diabetes Mellitus, Adult Onset,Diabetes Mellitus, Adult-Onset,Diabetes Mellitus, Ketosis Resistant,Diabetes Mellitus, Ketosis-Resistant,Diabetes Mellitus, Maturity Onset,Diabetes Mellitus, Maturity-Onset,Diabetes Mellitus, Non Insulin Dependent,Diabetes Mellitus, Non-Insulin-Dependent,Diabetes Mellitus, Noninsulin Dependent,diabetes mellitus, noninsulin-dependent,Diabetes Mellitus, Slow Onset,Diabetes Mellitus, Slow-Onset,Diabetes Mellitus, Stable,Diabetes Mellitus, Type 2,diabetes mellitus, type 2,diabetes mellitus, type 2, protection against,Diabetes Mellitus, Type II,Diabetes, Type 2,diabetes, type 2,insulin resistance, susceptibility to,Ketosis-Resistant Diabetes Mellitus,Maturity Onset Diabetes Mellitus,maturity-onset diabetes,Maturity-Onset Diabetes Mellitus,MODY,NIDDM,Non-Insulin Dependent Diabetes,non-insulin dependent diabetes,Non-Insulin Dependent Diabetes Mellitus,non-insulin dependent diabetes mellitus,non-insulin-dependent diabetes mellitus,noninsulin dependent diabetes,noninsulin-dependent diabetes mellitus,Slow-Onset Diabetes Mellitus,Stable Diabetes Mellitus,T2DM - Type 2 Diabetes mellitus,T2DM - type 2 diabetes mellitus,Type 2 Diabetes,type 2 diabetes,Type 2 Diabetes Mellitus,type 2 diabetes mellitus,Type 2 Diabetes Mellitus Non-Insulin Dependent,type 2 diabetes mellitus non-insulin dependent,Type II Diabetes,type II diabetes,type II diabetes mellitus,Type II diabetes mellitus
- 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
- diabetic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Type 2 diabetic patients undergoing vitrectomy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics in the 6 months prior to enrollment
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.6
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2023-12-30
Source: Figure 5
Description: Figure 5. Comparative analysis of the microbial communities of groups with and without diabetes at the phylum (A) and genus (B) levels using the linear discriminant analysis (LDA) effect size (LEfSe) method. LDA scores (log 10) for the most prevalent taxa in diabetic patients are represented on the positive scale, whereas LDA-negative scores indicate enriched taxa in the healthy controls.
Abundance in Group 1: increased abundance in diabetic
Revision editor(s): Mary Bearkland, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2023-12-30
Source: Figure 5
Description: Figure 5. Comparative analysis of the microbial communities of groups with and without diabetes at the phylum (A) and genus (B) levels using the linear discriminant analysis (LDA) effect size (LEfSe) method. LDA scores (log 10) for the most prevalent taxa in diabetic patients are represented on the positive scale, whereas LDA-negative scores indicate enriched taxa in the healthy controls.
Abundance in Group 1: decreased abundance in diabetic
Revision editor(s): Mary Bearkland, Boadiwaa
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