Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- 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
- Normal healthy (NDM) children
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diabetic children with Dry Eye Disease
- 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
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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
Source: Figure 3g and text
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
Revision editor(s): Mary Bearkland
Signature 2
Source: Figure 3g
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
NCBI | Quality Control | Links |
---|---|---|
Vibrio vulnificus | ||
Salmonella enterica | ||
Enterobacter mori | ||
Cordyceps militaris | ||
Leuconostoc sp. DORA_2 |
Revision editor(s): Mary Bearkland
Experiment 2
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
Source: Text on page 5
Description: At the phylum level, the abundance of Apicomplexa, Actinobacteria, Chlamydiae and Ascomycota in the DM-DE group was significantly higher than that in the NDM group. The abundance of Firmicutes and Proteobacteria in the NDM group was significantly higher than that in the DM-DE group. At the genus level, the abundance of Plasmodium, Mycobacterium, Escherichia, Vibrio, Leuconostoc, Chlamydia and Enterobacter in the DM-DE group was significantly higher than that in the NDM group. The abundance of Enterococcus, Streptococcus, Staphylococcus and Acinetobacter in the NDM group was significantly higher than that in the DM-DE group. At the species level, the abundance of P. ovale, E. coli, S. enterica, M. leprae, L. sp. DORA_2 and C. trachomatis in the DM-DE group were significantly higher than those in the NDM group. The abundance of E. faecalis, S. pneumoniae, S. aureus and A. johnsonii in the NDM group was significantly higher than that in the DM-DE group.
Abundance in Group 1: increased abundance in Diabetic children with Dry Eye Disease
Revision editor(s): Mary Bearkland
Signature 2
Source: Text on page 5
Description: At the phylum level, the abundance of Apicomplexa, Actinobacteria, Chlamydiae and Ascomycota in the DM-DE group was significantly higher than that in the NDM group. The abundance of Firmicutes and Proteobacteria in the NDM group was significantly higher than that in the DM-DE group. At the genus level, the abundance of Plasmodium, Mycobacterium, Escherichia, Vibrio, Leuconostoc, Chlamydia and Enterobacter in the DM-DE group was significantly higher than that in the NDM group. The abundance of Enterococcus, Streptococcus, Staphylococcus and Acinetobacter in the NDM group was significantly higher than that in the DM-DE group. At the species level, the abundance of P. ovale, E. coli, S. enterica, M. leprae, L. sp. DORA_2 and C. trachomatis in the DM-DE group were significantly higher than those in the NDM group. The abundance of E. faecalis, S. pneumoniae, S. aureus and A. johnsonii in the NDM group was significantly higher than that in the DM-DE group.
Abundance in Group 1: decreased abundance in Diabetic children with Dry Eye Disease
NCBI | Quality Control | Links |
---|---|---|
Pseudomonadota | ||
Bacillota | ||
Enterococcus | ||
Streptococcus | ||
Staphylococcus | ||
Acinetobacter | ||
Enterococcus faecalis | ||
Streptococcus pneumoniae | ||
Staphylococcus aureus | ||
Acinetobacter johnsonii |
Revision editor(s): Mary Bearkland