Gut metagenome in IBS-D, depression and comorbidity, China
149 fecal metagenome samples from adults in China, comparing IBS-D (n=22), depression (n=15), comorbid IBS-D/depression (n=13), and healthy controls (n=15) in a case-control design. machine-written summary
149 samples · 149 runs · CN · Age unknown · 2020 · 6.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 596 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 112 sample values (health condition detail) |
| ✓ Full text | 149 sample values (antibiotic exposure) · PMC7658686, PMC9040671 |
| ✓ Supplementary tables | 182 sample values (age, bmi, health condition, health condition detail, sex) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 149 | 100% | ||||
| country | 149 | 100% | 149 | |||
| health_condition | 37 | 25% | 37 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 149 | 100% | 149 | |||
| collection_date | 149 | 100% | 149 | |||
| health_condition_detail | 149 | 100% | 37 | 112 | ||
| latitude | 149 | 100% | 149 | |||
| longitude | 149 | 100% | 149 | |||
| age_at_collection_days | 37 | 25% | 37 | |||
| sex | 37 | 25% | 37 | |||
| bmi | 34 | 23% | 34 |
- Multiomics Study of Gut Bacteria and Host Metabolism in Irritable Bowel Syndrome and Depression Patients. 2020 PMID 33194817 PMC7658686 own_data
- More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome. 2022 PMID 35493727 PMC9040671 unsure
Archive description
Fecal metagenome-wide sequencing in 65 individuals with IBS-D (n=22), depression (n=15), comorbid patients (n=13), and healthy controls (n=15).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “gut metagenome”
- body site study.title · “gut metagenome of HC, IBS, DEP”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7372206 | age_at_collection_days | 23010.8 | R2 | 0.85 | paper.supp.DataSheet_1.zip/additional_datasheets/table_s4_sample_info_update.xlsx[sample_info!Age (Years)] | 63 |
| SAMEA7372206 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | use of antibiotics or antidepressant during the previous month |
| SAMEA7372206 | bmi | 21.26 | R2 | 0.85 | paper.supp.DataSheet_1.zip/additional_datasheets/table_s4_sample_info_update.xlsx[sample_info!BMI (kg/m_)] | 21.2585034 |
| SAMEA7372206 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA7372206 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA7372206 | health_condition | ibs | R2 | 0.85 | paper.supp.DataSheet_1.zip/additional_datasheets/table_s4_sample_info_update.xlsx[sample_info!Subject Health Status] | IBS |
| SAMEA7372206 | health_condition_detail | IBS | R2 | 0.85 | paper.supp.DataSheet_1.zip/additional_datasheets/table_s4_sample_info_update.xlsx[sample_info!Subject Health Status] | IBS |
| SAMEA7372210 | health_condition_detail | mixed_case_control: IBS-D vs depression vs comorbid vs healthy controls | R4 | 0.40 | study.description | 65 individuals with IBS-D (n=22), depression (n=15), comorbid patients (n=13), and healthy |
| SAMEA7372206 | latitude | 39.9000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.90 N 116.40 E |
| SAMEA7372206 | longitude | 116.4000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.90 N 116.40 E |
| SAMEA7372206 | sex | male | R2 | 0.85 | paper.supp.DataSheet_1.zip/additional_datasheets/table_s4_sample_info_update.xlsx[sample_info!Gender] | male |
Sequencing
149 runs over 149 samples · mean 7.08 Gbp per run (median 6.96 Gbp, total 1,054.72 Gbp; 149 runs with a base count) · layout PAIRED 149 · platform ILLUMINA 149 · models Illumina HiSeq 2000 (149) · 0% of runs with a Sandpiper profile · first public 2020-10-06
Authors (22)
Xu C first · Jia Q · Zhang L · Wang Z · Zhu S · Wang X · Liu Y · Li M · Zhang J · Sun Q · Wang K · Zhu H · Duan L last · Wang C · Guo Q · Xie Z · Tan J · Wu S · Wang P · Guo J · Fang Z · Jiang X
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB40628.csv.gz (4.8 KB) · parquet (77.1 KB) — all 149 samples, every field with route and confidence · PRJEB40628_determinations.csv.gz (7.9 KB) — 1,039 evidence rows