Fecal microbiome in CVID vs housemates, Brno, Czech Republic
12 fecal metagenome samples from adults in Brno, Czech Republic, comparing CVID (common variable immunodeficiency) patients without GI symptoms to healthy housemates, in a case-control design. machine-written summary
12 samples · 12 runs · CZ · Adult · 2021 · 111.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 72 sample values (collection date, country, latitude, location locality, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8163231 |
| ✓ Supplementary tables | 72 sample values (age, antibiotic exposure, bmi, health condition, health condition detail, sex) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
households — not resolved
6 CVID patients paired with their healthy housemates (household pairs), 12 samples total.
Genera, mean relative abundance over 10 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 | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 12 | 100% | 12 | |||
| age_at_collection_days | 12 | 100% | 12 | |||
| antibiotic_exposure | 12 | 100% | 12 | |||
| bmi | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| detailed_location | 12 | 100% | ||||
| health_condition_detail | 12 | 100% | 12 | |||
| latitude | 12 | 100% | 12 | |||
| location_locality | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 | |||
| sex | 12 | 100% | 12 |
- Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates. 2021 PMID 34054845 PMC8163231 own_data
Archive description
Data from the project: "Analysis of gastrointestinal microbiome in patients with primary immune deficiencies".
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.description · “project: "Analysis of gastrointestinal microbiome in patients”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16339632 | age_at_collection_days | 24472.0 | R2 | 0.85 | paper.supp.Table_1.xlsx[List1!Age] | 67 |
| SAMN16339632 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.Table_1.xlsx[List1!ATB treatment] | Yes (>1 month) |
| SAMN16339632 | bmi | 24.80 | R2 | 0.85 | paper.supp.Table_1.xlsx[List1!BMI] | 24.8 |
| SAMN16339632 | collection_date | 2016/2017 | R1 | 0.90 | biosample.attribute:collection_date | 2016/2017 |
| SAMN16339632 | country | CZ | R1 | 0.90 | sample.attr.geo_loc_name | Czech Republic:Brno |
| SAMN16339632 | health_condition | healthy_control | R2 | 0.85 | paper.supp.Table_1.xlsx[List1!Diagnosis] | Healthy |
| SAMN16339632 | health_condition_detail | Healthy | R2 | 0.85 | paper.supp.Table_1.xlsx[List1!Diagnosis] | Healthy |
| SAMN16339632 | latitude | 49.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 49.2 N 16.6 E |
| SAMN16339632 | location_locality | Brno | R1 | 0.85 | biosample.attribute:geo_loc_name | Czech Republic:Brno |
| SAMN16339632 | longitude | 16.6000 | R1 | 0.90 | biosample.attribute:lat_lon | 49.2 N 16.6 E |
| SAMN16339632 | sex | male | R2 | 0.85 | paper.supp.Table_1.xlsx[List1!Sex] | Male |
| SAMN16339632 | subject_id | PID002 | R1 | 0.85 | biosample.attribute:source_material_id | PID002 |
Sequencing
12 runs over 12 samples · mean 110.50 Gbp per run (median 111.01 Gbp, total 1,325.98 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina HiSeq 1500 (12) · 83% of runs with a Sandpiper profile · first public 2021-05-15
Authors (9)
Bosák J first · Lexa M · Fiedorová K · Gadara DC · Micenková L · Spacil Z · Litzman J · Freiberger T · Šmajs D last
Downloads
PRJNA666684.csv.gz (1.4 KB) · parquet (71.2 KB) — all 12 samples, every field with route and confidence · PRJNA666684_determinations.csv.gz (2.0 KB) — 144 evidence rows