Gut microbiome in retinal artery occlusion, Switzerland
Case-control study of 59 gut metagenome samples from Switzerland, comparing patients with non-arteritic retinal artery occlusion to age- and sex-matched healthy controls. machine-written summary
59 samples · 59 runs · CH · Age unknown · 2019 · 7.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 355 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 177 sample values (location locality, location site, subject id) · PMC10202153, PMC6814871, PMC7463023, PMC8523055 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 117 sample values (antibiotic exposure, health condition, health condition detail) · from GMrepo v3, Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 54 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 | 59 | 100% | 59 | |||
| health_condition | 59 | 100% | 30 | 29 | ||
| subject_id | 59 | 100% | 59 | |||
| antibiotic_exposure | 59 | 100% | 59 | |||
| collection_date | 59 | 100% | 59 | |||
| detailed_location | 59 | 100% | ||||
| health_condition_detail | 59 | 100% | 30 | 29 | ||
| latitude | 59 | 100% | 59 | |||
| location_locality | 59 | 100% | 59 | |||
| location_region | 59 | 100% | 59 | |||
| location_site | 59 | 100% | 59 | |||
| longitude | 59 | 100% | 59 |
- Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels. 2019 PMID 31653902 PMC6814871 own_data
- 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
Purpose: Retinal artery occlusion usually occurs on a background of atherosclerotic disease and patients are at risk for cerebral stroke and ischemic heart disease. Atherosclerosis has been associated with alterations in the intestinal microbiome. Methods: Twenty nine patients with clinically confirmed non-arteritic retinal artery occlusion and 30 age- and sex-matched controls were included. The gut metagenome was sequenced using metagenomic shotgun sequencing following standard pipelines of the Illumina HiSeq 3000 platform. The taxonomic composition of the gut microbiomes was described and the functional profiles of the identified microbes were identified. Results: On the phylum level, the relative abundance of Bacteriodetes was decreased in patients with retinal artery occlusion (39.2 ± 16.7%) compared to controls (46.7 ± 17.6%) whereas the opposite applied for the phylum of Firmicutes (39.6 ± 20.0% in RAO and 40.8 ± 16.0% (s.d.) in controls). Several genera and species such as Actinobacter, Bacteroides stercoris, Faecalibacterium prausnitzii were relatively enriched in patients with retinal artery occlusion, whereas others such as Odoribacter or Lachnospiraceae were significantly lower. Patient’s gut microbiomes were enriched in genes of the cholesterol metabolism pathway. Conclusions: Alterations in the gut microbiome are associated with retinal artery occlusion, suggesting that retinal artery occlusion could be targeted by microbiome-altering interventions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “gut metagenome was sequenced using metagenomic shotgun sequencing”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104500027 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMEA104500027 | collection_date | 2015-11-23 | R1 | 0.90 | biosample.attribute:collection_date | 2015-11-23 |
| SAMEA104500027 | country | CH | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Switzerland |
| SAMEA104500056 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | control |
| SAMEA104500027 | health_condition | other_disease | R2 | 0.75 | external.gmrepo source | phenotype: Retinal Artery Occlusion |
| SAMEA104500056 | health_condition_detail | control | R1 | 0.85 | biosample.attribute:description | control |
| SAMEA104500027 | health_condition_detail | Retinal Artery Occlusion | R2 | 0.75 | external.gmrepo source | phenotype: Retinal Artery Occlusion |
| SAMEA104500027 | latitude | 46.9167 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA104500027 | location_locality | Bern | R3 | 0.70 | paper.fulltext.methods | University Hospital Bern (Inselspital), Switzerland |
| SAMEA104500027 | location_region | Bern | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA104500027 | location_site | Department of Ophthalmology, University Hospital Bern (Inselspital) | R3 | 0.70 | paper.fulltext.methods | recruited from the Department of Ophthalmology of the University Hospital Bern |
| SAMEA104500027 | longitude | 7.4667 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.9167 7.4667 |
| SAMEA104500027 | subject_id | SAMEA104500027 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Participants (n = 59) were recruited from the Department of Ophthalmology |
Sequencing
59 runs over 59 samples · mean 8.30 Gbp per run (median 7.42 Gbp, total 489.85 Gbp; 59 runs with a base count) · layout PAIRED 59 · platform ILLUMINA 59 · models Illumina HiSeq 3000 (59) · 92% of runs with a Sandpiper profile · first public 2019-03-21
Authors (43)
Zysset-Burri DC first · Keller I · Berger LE · Neyer PJ · Steuer C · Wolf S · Zinkernagel MS last · Largiadèr CR · Wittwer M · 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
Downloads
PRJEB24557.csv.gz (2.8 KB) · parquet (73.7 KB) — all 59 samples, every field with route and confidence · PRJEB24557_determinations.csv.gz (5.9 KB) — 649 evidence rows