Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy
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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
Huang Y, Wang Z, Ma H, Ji S, Chen Z, Cui Z, Chen J, Tang S
Journal
Frontiers in cellular and infection microbiology
Year
2021
Keywords:
16S rRNA gene sequence, diabetes mellitus, diabetic retinopathy, gut microbiota, human
The pathogenesis of type 2 diabetes mellitus (T2DM) is commonly associated with altered gut bacteria. However, whether the microbial dysbiosis that exists in human diabetic patients with or without retinopathy is different remains largely unknown. Here, we collected clinical information and fecal samples from 75 participants, including 25 diabetic patients without retinopathy (DM), 25 diabetic patients with retinopathy (DR), and 25 healthy controls (HC). The gut microbial composition in the three groups was analyzed using 16S ribosomal RNA (rRNA) gene sequencing. Microbial structure and composition differed in the three groups. The α and β diversities in both the DM and DR groups were reduced compared with those in the HC group. Blautia was the most abundant genus, especially in the DM group. In addition, increased levels of Bifidobacterium and Lactobacillus and decreased levels of Escherichia-Shigella, Faecalibacterium, Eubacterium_hallii_group and Clostridium genera were observed in the DM and DR groups compared with the HC group. Furthermore, a biomarker set of 25 bacterial families, which could distinguish patients in the DR group from those in the DM and HC groups was identified, with the area under the curve values ranging from 0.69 to 0.85. Of note, Pasteurellaceae, which was increased in DM and decreased in DR compared with HC, generated a high AUC (0.74) as an individual predictive biomarker. Moreover, 14 family biomarkers were associated with fasting blood glucose levels or diabetes, with most of them being negatively correlated. In summary, our study establishes compositional alterations of gut microbiota in DM and DR, suggesting the potential use of gut microbiota as a non-invasive biomarker for clinical and differential diagnosis, as well as identifying potential therapeutic targets of diabetic retinopathy.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-15
Curated date: 2023/10/29
Curator: Chinelsy
Revision editor(s): Chinelsy, Peace Sandy, 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Retinopathy eye disease of retina,retina eye disease,retinal disease,retinopathy,Retinopathy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- diabetes mellitus (DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who identify as diabetic patients without retinopathy (DM)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- 2.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-15
Source: Fig.4
Description: Relative abundance of the bacterial community in diabetic patients without retinopathy (DM) and healthy controls (HC)
Abundance in Group 1: increased abundance in diabetes mellitus (DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Megasphaera | ||
| Parabacteroides | ||
| Pasteurellaceae | ||
| Pasteurellales | ||
| Streptococcaceae | ||
| Tannerellaceae | ||
| Veillonella | ||
| unclassified Bacilli |
Revision editor(s): Chinelsy, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-15
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- diabetes mellitus (DM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- diabetes retinopathy (DR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who identify as diabetic patients with retinopathy (DR)
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
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 ChiomaBlessing on 2023-12-18
Source: Supplemental. Table S6
Description: Relative abundance between diabetes retinopathy and diabetes mellitus based on the biomarker families correlated with fasting blood sugar (FBG) and duration of type 2 diabetes (T2Dyear)
Abundance in Group 1: decreased abundance in diabetes retinopathy (DR)
| NCBI | Quality Control | Links |
|---|---|---|
| Pasteurellaceae |
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-18
Source: Supplemental. Table S6
Description: Relative abundance between diabetes retinopathy and diabetes mellitus based on the biomarker families correlated with fasting blood sugar (FBG) and duration of type 2 diabetes (T2Dyear)
Abundance in Group 1: increased abundance in diabetes retinopathy (DR)
| NCBI | Quality Control | Links |
|---|---|---|
| UCG-010UCG-010 |
Revision editor(s): ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-15
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls (HC)
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-18
Source: Fig.4
Description: Relative abundance of the bacterial community in diabetic patients with retinopathy (DR) compared to healthy controls (HC)
Abundance in Group 1: increased abundance in diabetes retinopathy (DR)
Revision editor(s): Chinelsy, MyleeeA, ChiomaBlessing
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