Alterations of the intestinal microbiota in age-related macular degeneration/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-8-1
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
- 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 diagnosed with age-related macular degeneration
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- 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
- 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
- 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
- 2.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-8-1
Source: Figure 3A, B
Description: Fecal microbiota profile in the both groups at different taxonomic levels
Abundance in Group 1: increased abundance in AMD (Age-related macular degeneration)
| NCBI | Quality Control | Links |
|---|---|---|
| [Eubacterium] siraeum | ||
| Negativicutes | ||
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Bacteroidota | ||
| Bacteroidia | ||
| Bacteroidales | ||
| Bacteroidaceae | ||
| Bacteroides |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-8-1
Source: Figure 3A, B
Description: Fecal microbiota profile in the both groups at different taxonomic levels
Abundance in Group 1: decreased abundance in AMD (Age-related macular degeneration)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Bacillota | ||
| Blautia | ||
| Candidatus Saccharimonadaceae | ||
| Clostridia | ||
| Lachnospiraceae | ||
| Lachnospirales |
Revision editor(s): Anne-mariesharp
