Gut microbiome in AMD vs controls, Switzerland (case-control)
23 gut metagenome samples from elderly Swiss adults (12 with age-related macular degeneration, 11 healthy controls) in a case-control study of gut microbiome composition and function in AMD. machine-written summary
23 samples · 23 runs · CH · Elderly · 2017 · 4.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 195 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 23 sample values (location locality) · PMC5240106 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 23 sample values (antibiotic exposure) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
11 of 12 people sampled more than once (22 samples; median 2, up to 2 per person) · follow-up median 2 mo (max 5 mo) · median interval between samples 2 mo (time from collection dates).
Each row is one person (11 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 23 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 23 | 100% | ||||
| country | 23 | 100% | 23 | |||
| health_condition | 23 | 100% | 23 | |||
| subject_id | 23 | 100% | 23 | |||
| antibiotic_exposure | 23 | 100% | 23 | |||
| collection_date | 23 | 100% | 23 | |||
| detailed_location | 23 | 100% | ||||
| health_condition_detail | 23 | 100% | 23 | |||
| latitude | 23 | 100% | 23 | |||
| location_locality | 23 | 100% | 23 | |||
| location_region | 23 | 100% | 23 | |||
| longitude | 23 | 100% | 23 | |||
| intervention | 11 | 48% | 11 |
- Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration. 2017 PMID 28094305 PMC5240106 own_data
- The importance of age in compositional and functional profiling of the human intestinal microbiome. 2021 PMID 34662347 PMC8523055 unsure
- Metagenomic Sequencing Analysis Identifies Cross-Cohort Gut Microbial Signatures Associated With Age-Related Macular Degeneration. 2023 PMID 37195657 PMC10202153 unsure
Archive description
Age-dependent 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 gut microbiome is associated with metabolic diseases through modulation of inflammation and host metabolism. To investigate whether compositional and functional alterations of the gut 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 gut 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 alterations in the gut microbiome are associated with AMD and that the interdependency between amino and fatty acid metabolism and AMD could be targeted by microbiome-altering interventions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly by opus_adjudicated with confidence 0.55. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- host study.description · “patients with AMD and controls”
- body site study.description · “sequenced the gut metagenomes”
- life stage study.description · “most frequent cause of blindness in the elderly”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA3950597 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMEA3950597 | collection_date | 2014-06-04 | R1 | 0.90 | biosample.attribute:collection_date | 2014-06-04 |
| SAMEA3950597 | country | CH | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Switzerland |
| SAMEA3950597 | health_condition | other_disease | R1 | 0.85 | biosample.attribute:description | patient |
| SAMEA3950597 | health_condition_detail | patient | R1 | 0.85 | biosample.attribute:description | patient |
| SAMEA3950609 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:description | control |
| SAMEA3950597 | latitude | 46.9167 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA3950597 | location_locality | Bern | R3 | 0.70 | paper.fulltext.methods | Department of Ophthalmology of the University Hospital Bern |
| SAMEA3950597 | location_region | Bern | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA3950597 | longitude | 7.4667 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA3950597 | subject_id | 01 | R1 | 0.70 | sample.name_rule:alias | AMD-01 |
Sequencing
23 runs over 23 samples · mean 4.10 Gbp per run (median 4.10 Gbp, total 94.30 Gbp; 23 runs with a base count) · layout PAIRED 23 · platform ILLUMINA 23 · models Illumina HiSeq 2000 (23) · 100% of runs with a Sandpiper profile · first public 2017-03-27
Authors (25)
Zinkernagel MS first · Zysset-Burri DC · Keller I · Berger LE · Leichtle AB · Largiadèr CR · Fiedler GM · Wolf S last · Herzog EL first · Wäfler M · Xue W first · Peng P · Wen X · Meng H · Qin Y · Deng T · Guo S · Chen T · Li X · Liang J · Zhang F · Xie Z · Jin M · Liang Q · Wei L last
Downloads
PRJEB13835.csv.gz (1.3 KB) · parquet (71.1 KB) — all 23 samples, every field with route and confidence · PRJEB13835_determinations.csv.gz (2.9 KB) — 241 evidence rows