Gut microbiota in C. difficile infection, case-control study
205 faecal samples from a single hospital, comparing gut microbiota of symptomatic C. difficile infection patients to controls, in a case-control design. machine-written summary
205 samples · 205 runs · Age unknown · 2019 · 2.45 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 409 sample values (health condition detail, subject id) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
Genera, mean relative abundance over 187 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 | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 205 | 100% | 205 | |||
| health_condition_detail | 204 | 100% | 204 |
Archive description
Clostridium difficile is the leading cause of healthcare-associated infectious diarrhoea. C. difficile infection (CDI) is mainly associated with the disruption in gut microbiota caused by excessive use of antibiotics. To understand the dynamics of gut microbes during and after CDI, we collected human faecal samples from symptomatic patients of a single hospital and compared the microbiota compostion of symptomatic patients with the microbiota composition of different controls.
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 study.description · “we collected human faecal samples from symptomatic patients”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104565211 | health_condition_detail | Human Gut Microbiota | R1 | 0.90 | sample.attr.arrayexpress_phenotype | Human Gut Microbiota |
| SAMEA104403803 | subject_id | 4998STDY7114333 | R1 | 0.85 | sample.attr.subject_id | 4998STDY7114333 |
Sequencing
205 runs over 205 samples · mean 2.49 Gbp per run (median 2.45 Gbp, total 510.20 Gbp; 205 runs with a base count) · layout PAIRED 205 · platform ILLUMINA 205 · models Illumina HiSeq 2500 (205) · 91% of runs with a Sandpiper profile · first public 2019-01-22 – 2019-03-19
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJEB23010.csv.gz (5.7 KB) · parquet (77.4 KB) — all 205 samples, every field with route and confidence · PRJEB23010_determinations.csv.gz (3.1 KB) — 409 evidence rows