Gut microbiome in AMD vs controls, Switzerland
Shotgun metagenomic case-control study of 90 fecal samples from Switzerland, comparing individuals with age-related macular degeneration (57 samples) to healthy controls (33 samples). machine-written summary
90 samples · 90 runs · CH · Age unknown · 2020 · 6.65 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 630 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 90 sample values (antibiotic exposure) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 81 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 | 0 | 0% | ||||
| country | 90 | 100% | 90 | |||
| health_condition | 90 | 100% | 90 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 90 | 100% | 90 | |||
| collection_date | 90 | 100% | 90 | |||
| detailed_location | 90 | 100% | ||||
| health_condition_detail | 90 | 100% | 90 | |||
| latitude | 90 | 100% | 90 | |||
| location_region | 90 | 100% | 90 | |||
| longitude | 90 | 100% | 90 |
- Associations of the intestinal microbiome with the complement system in neovascular age-related macular degeneration. 2020 PMID 32922859 PMC7463023 unsure
- 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
Background: Age-related macular degeneration (AMD) is a leading cause of severe vision loss in the aged population. The etiology of AMD is multifactorial and includes nutritional factors, genetic variants mainly in the complement pathway, environmental risk factors and alterations in the intestinal microbiome. However, it remains largely unexplored whether there is an interdependency of these factors leading to the development of AMD. To investigate this issue, a comprehensive shotgun metagenomics analysis of 57 AMD and 58 healthy controls as well as of 16 complement C3 deficient mice and 16 wildtypes was performed. Single nucleotide polymorphisms (SNPs) in the complement factors were assessed with pre-designed TaqMan® SNP genotyping assays.Results: The composition of the intestinal microbiome differed significantly between AMD patients and controls. Whereas the class Negativicutes was more abundant in patients, the genus Oscillibacter and Bacteroides species had a significantly higher prevalence in persons without AMD. While SNPs within the complement factor B gene were more abundant in controls, SNPs within the high temperature requirement A serine peptidase 1 and complement factor H (CFH) genes were associated with AMD. Using a classification model, Negativicutes was identified as a potential biomarker for AMD and furthermore, it positively correlated with CFH. In addition, similar taxonomic features were identified that distinguished wildtype mice from C3 deficient mice. Conclusion: The composition of the intestinal microbiome differs between AMD patients and controls as well as between C3 deficient mice and wildtype mice. Moreover, since the phylum Firmicutes has been identified as potential biomarker for AMD and positively correlates with the genetic risk factor CFH, the study suggests an association between the intestinal microbiome and the complement system in AMD.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- host study.description · “57 AMD and 58 healthy controls”
- body site study.title · “intestinal microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6262637 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMEA6262637 | collection_date | 2016-07-25 | R1 | 0.90 | biosample.attribute:collection_date | 2016-07-25 |
| SAMEA6262637 | country | CH | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Switzerland |
| SAMEA6262637 | health_condition | other_disease | R1 | 0.85 | biosample.attribute:description | patient |
| SAMEA6262637 | health_condition_detail | Age-related macular degeneration (AMD) patient | R1 | 0.85 | biosample.attribute:description | patient |
| SAMEA6262637 | latitude | 46.9167 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA6262637 | location_region | Bern | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA6262637 | longitude | 7.4667 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
Sequencing
90 runs over 90 samples · mean 6.74 Gbp per run (median 6.65 Gbp, total 606.60 Gbp; 90 runs with a base count) · layout PAIRED 90 · platform ILLUMINA 90 · models Illumina HiSeq 3000 (90) · 90% of runs with a Sandpiper profile · first public 2020-08-30
Authors (41)
Zysset-Burri DC first · Keller I · Berger LE · Largiadèr CR · Wittwer M · Wolf S · Zinkernagel MS 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 · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJEB35615.csv.gz (3.3 KB) · parquet (73.9 KB) — all 90 samples, every field with route and confidence · PRJEB35615_determinations.csv.gz (6.0 KB) — 720 evidence rows