Gut metagenome in cavernous angioma, case-control, USA
154 gut metagenome samples from USA subjects with cavernous angioma (127) and healthy controls (27), using shotgun sequencing in a case-control design to find microbiome signatures linked to disease severity and hemorrhage. machine-written summary
154 samples · 154 runs · US · Age unknown · 2020 · 1.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,024 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11264914, PMC11748132, PMC7253448, PMC9984539 |
| ✓ Supplementary tables | 381 sample values (age, sex, subject id) |
| ✓ External resources | 54 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
5 of 122 people sampled more than once (10 samples; median 2, up to 2 per person) · follow-up median 2 mo (max 10 mo) · median interval between samples 2 mo (time from age at collection).
Each row is one person (5 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 138 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 | 126 | 82% | ||||
| country | 154 | 100% | 154 | |||
| health_condition | 154 | 100% | 127 | 27 | ||
| subject_id | 127 | 82% | 127 | |||
| collection_date | 154 | 100% | 154 | |||
| detailed_location | 154 | 100% | ||||
| health_condition_detail | 154 | 100% | 127 | 27 | ||
| latitude | 154 | 100% | 154 | |||
| location_region | 154 | 100% | 154 | |||
| longitude | 154 | 100% | 154 | |||
| age_at_collection_days | 127 | 82% | 127 | |||
| sex | 127 | 82% | 127 |
- Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma. 2020 PMID 32461638 PMC7253448 own_data
- Plasma metabolites with mechanistic and clinical links to the neurovascular disease cavernous angioma. 2023 PMID 36869161 PMC9984539 own_data
- Unassigning bacterial species for microbiome studies. 2024 PMID 38912768 PMC11264914 own_data
- Circulating molecules reflect imaging biomarkers of hemorrhage in cerebral cavernous malformations. 2025 PMID 39829356 PMC11748132 own_data
Archive description
Cavernous angiomas (CA) are common vascular anomalies causing brain hemorrhage. Based on mouse studies, roles of gram-negative bacteria and altered intestinal homeostasis have been implicated in CA pathogenesis and pilot study had suggested potential microbiome differences between non-CA and CA individuals based on 16S rRNA gene sequencing. We here assess microbiome differences in a larger cohort of human subjects with and without CA, and among subjects with different clinical features, and conduct more definitive microbial analyses using metagenomic shotgun sequencing. Relative abundance of distinct bacterial species in CA patients is shown, consistent with postulated permissive microbiome driving CA lesion genesis via lipopolysaccharide signaling, in humans as in mice. Other microbiome differences are related to CA clinical behavior.
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 study.description · “human subjects with and without CA”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14786404 | age_at_collection_days | 25932.8 | R2 | 0.80 | paper.supp.41467_2020_16436_MOESM3_ESM.zip::Patient_Matrix.xlsx[CA patient][nan] | 71 |
| SAMN14786377 | collection_date | 2010-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2010-01-01T09:00:00Z |
| SAMN14786377 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN14786404 | health_condition | other_disease | R1 | 0.90 | biosample_attr | Cavernous Angioma |
| SAMN14786377 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN14786404 | health_condition_detail | Cavernous Angioma | R1 | 0.90 | sample.attr.host_disease | Cavernous Angioma |
| SAMN14786377 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN14786377 | latitude | 41.7890 | R1 | 0.90 | biosample.attribute:lat_lon | 41.789 N 87.602 W |
| SAMN14786377 | location_region | Illinois | R1 | 0.60 | biosample.attribute:lat_lon | 41.789 N 87.602 W |
| SAMN14786377 | longitude | -87.6020 | R1 | 0.90 | biosample.attribute:lat_lon | 41.789 N 87.602 W |
| SAMN14786404 | sex | female | R2 | 0.80 | paper.supp.41467_2020_16436_MOESM3_ESM.zip::Patient_Matrix.xlsx[CA patient][nan] | F |
| SAMN14786404 | subject_id | 09385-011 | R2 | 0.80 | paper.supp.41467_2020_16436_MOESM3_ESM.zip::Patient_Matrix.xlsx[CA patient][nan] | 09385-011 |
Sequencing
154 runs over 154 samples · mean 1.73 Gbp per run (median 1.71 Gbp, total 266.72 Gbp; 154 runs with a base count) · layout PAIRED 154 · platform ILLUMINA 154 · models Illumina HiSeq 2500 (154) · 90% of runs with a Sandpiper profile · first public 2020-05-03
Authors (60)
Polster SP first · Sharma A · Tanes C · Tang AT · Mericko P · Cao Y · Carrión-Penagos J · Girard R · Koskimäki J · Zhang D · Stadnik A · Romanos SG · Lyne SB · Shenkar R · Yan K · Lee C · Akers A · Morrison L · Robinson M · Zafar A · Bittinger K · Kim H · Gilbert JA · Kahn ML · Shen L · Awad IA last · Srinath A first · Xie B · Li Y · Sone JY · Romanos S · Chen C · Polster S · Dorrestein PC · Weldon KC · DeBiasse D · Moore T · Lightle R · Piedad K · Hagan M · Shkoukani A · Bi D · Ji Y · Sidebottom A · Pamer E · D'Souza M · Sulakhe D · Tu V · Daniel S · Hage SF first · Bi DE · Kinkade S · Vera Cruz D · Jhaveri A · Bindal A · Little JC · Alcazar-Felix RJ · Lee J · Carroll TJ · Koskimaki J
Downloads
PRJNA629755.csv.gz (6.0 KB) · parquet (78.5 KB) — all 154 samples, every field with route and confidence · PRJNA629755_determinations.csv.gz (12.1 KB) — 1,459 evidence rows