Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration
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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 Uniform resource identifier for web resources.
Authors
Zinkernagel MS, Zysset-Burri DC, Keller I, Berger LE, Leichtle AB, Largiadèr CR, Fiedler GM, Wolf S
Journal
Scientific reports
Year
2017
Age-related macular degeneration (AMD) is the most frequent cause of blindness in the elderly. There is evidence that nutrition, inflammation and genetic risk factors play an important role in the development of AMD. Recent studies suggest that the composition of the intestinal microbiome is associated with metabolic diseases through modulation of inflammation and host metabolism. To investigate whether compositional and functional alterations of the intestinal microbiome are associated with AMD, we sequenced the gut metagenomes of patients with AMD and controls. The genera Anaerotruncus and Oscillibacter as well as Ruminococcus torques and Eubacterium ventriosum were relatively enriched in patients with AMD, whereas Bacteroides eggerthii was enriched in controls. Patient's intestinal microbiomes were enriched in genes of the L-alanine fermentation, glutamate degradation and arginine biosynthesis pathways and decreased in genes of the fatty acid elongation pathway. These findings suggest that modifications in the intestinal microbiome are associated with AMD, inferring that this common sight threatening disease may be targeted by microbiome-altering interventions.
Experiment 1
Reviewed Marked as Reviewed by KateRasheed on 2025-6-24
Subjects
- Location of subjects
- Switzerland
- 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
- Age-related macular degeneration AAMD - Age related macular degeneration,AGE RELAT MACULOPATHIES,AGE RELAT MACULOPATHY,Age Related Macular Degeneration,age related macular degeneration,Age related macular degeneration (disorder) [Ambiguous],Age Related Maculopathies,age related Maculopathies,Age related maculopathy,age related maculopathy,age-related macular degeneration,Age-related macular degeneration (disorder),Age-Related Macular Degenerations,Age-Related Maculopathies,Age-Related Maculopathy,AMD,AMD - Age-related macular degeneration,Amended,ARMD,ARMD - Age-related macular degeneration,Degeneration, Age-Related Macular,Degeneration, Macular,Degenerations, Age-Related Macular,Degenerations, Macular,Dystrophies, Macular,Dystrophy, Macular,Macular Degeneration,Macular degeneration (disorder),Macular degeneration (senile) of retina, unspecified,MACULAR DEGENERATION NOS,Macular Degeneration, Age-Related,macular degeneration, age-related,Macular Degenerations,Macular Degenerations, Age-Related,Macular Dystrophies,Macular Dystrophy,MACULOPATHIES AGE RELAT,Maculopathies, Age Related,Maculopathies, Age-Related,MACULOPATHY AGE RELAT,Maculopathy, Age Related,Maculopathy, Age-Related,Senile macular degeneration,Senile macular degeneration of retina,Senile macular retinal degeneration,SMD - Senile macular degeneration,Unspecified senile macular degeneration,Age-related macular degeneration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AMD (Age-related macular degeneration)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with clinically confirmed recent onset of neovascular Age-related macular degeneration
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-6-24
Source: Figure 3b, c
Description: LEfSe analysis identifying differentially abundant taxa in neovascular Age-related macular degeneration patients compared to controls
Abundance in Group 1: increased abundance in AMD (Age-related macular degeneration)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Eubacterium ventriosum | ||
| Oscillibacter | ||
| Oscillospiraceae | ||
| [Ruminococcus] torques |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-6-24
Source: Figure 3b, c
Description: LEfSe analysis identifying differentially abundant taxa in neovascular Age-related macular degeneration patients compared to controls
Abundance in Group 1: decreased abundance in AMD (Age-related macular degeneration)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroides eggerthii |
Revision editor(s): Anne-mariesharp
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-6-24
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-6-24
Source: Figure 3d
Description: Box plots representing the mean abundance +/−SD of bacterial genera and species associated with Age-related macular degeneration
Abundance in Group 1: increased abundance in AMD (Age-related macular degeneration)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Eubacterium ventriosum | ||
| Oscillibacter | ||
| [Ruminococcus] torques |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-6-24
Source: Figure 3d
Description: Box plots representing the mean abundance +/−SD of bacterial genera and species associated with Age-related macular degeneration
Abundance in Group 1: decreased abundance in AMD (Age-related macular degeneration)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides eggerthii |
Revision editor(s): Anne-mariesharp
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