Microbiota in antibiotic-associated C. difficile infection
12 gut microbiota samples from Germany, case-control design, comparing antibiotic-treated patients with and without Clostridium difficile infection using 16S rRNA and metagenomic sequencing. machine-written summary
12 samples · 12 runs · DE · Age unknown · 2014 · 33.0 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 48 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 18 sample values (antibiotic exposure, health condition detail) |
| ✓ Full text | 15 sample values (health condition, health condition detail, intervention) · PMC4163665 |
| ✓ Supplementary tables | 24 sample values (subject id, timepoint) |
| – 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 |
intervention — arms not resolved
design observational_with_procedure · Antibiotic therapy; samples before, during, after AB treatment, CDI vs non-infected
longitudinal
3 of 3 people sampled more than once (12 samples; median 3, up to 7 per person) · follow-up median 16 d (max 38 d) · median interval between samples 6 d (time from timepoint labels). Schedule stated by the source: “Follow-up study; aliases suggest before/after sampling per patient (e.g., met_H_before, met_G_after, met_H35_D)” (time origin: other).
Each row is one person (3 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 6 | 50% | 6 | |||
| subject_id | 12 | 100% | 12 | |||
| antibiotic_exposure | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| health_condition_detail | 12 | 100% | 6 | 6 | ||
| latitude | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 | |||
| timepoint_label | 12 | 100% | 12 | |||
| intervention | 3 | 25% | 3 |
- Structural and functional changes in the gut microbiota associated to Clostridium difficile infection. 2014 PMID 25309515 PMC4163665 unsure
Archive description
We performed a follow-up study of the gut microbiota in patients treated with antibiotic therapy, whom developed Clostridium difficile infection as a consequence. We used the 16s rRNA and metagenomic approaches to gain insights in the effect of the pathogen infection in the structure and functions of the human gut microbiota.
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.title · “Human gut microbiota associated to Clostridium difficile”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA2395460 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | both patient groups having been treated with AB therapy |
| SAMEA2395460 | collection_date | 2009-08 | R1 | 0.90 | biosample.attribute:collection_date | 2009-08 |
| SAMEA2395460 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea_region | Germany |
| SAMEA2395461 | health_condition | gi_infection_or_diarrhoea | R3 | 0.80 | paper.body.Table 1[CD (+/−)] | + |
| SAMEA2395461 | health_condition_detail | + | R3 | 0.80 | paper.body.Table 1[CD (+/−)] | + |
| SAMEA2395460 | health_condition_detail | mixed_case_control: Clostridium difficile infected vs non-infected patients | R4 | 0.40 | paper.abstract | C. difficile infected (CDI) vs. non-infected patients |
| SAMEA2395460 | intervention | antibiotic | R3 | 0.80 | paper.body.Table 1[Antibiotic] | Amoxicillin/Ciprofloxacin/Clarithromycin |
| SAMEA2395460 | latitude | 52.5160 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.516 13.4 |
| SAMEA2395460 | longitude | 13.4000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.516 13.4 |
| SAMEA2395460 | subject_id | F | R2 | 0.85 | paper.body.Table 1[Patient] | F_before: patient F |
| SAMEA2395460 | timepoint_label | day 0 (before antibiotics) | R2 | 0.85 | paper.body.Table 1[Sampling date] | F_before: Day0—before AB |
Sequencing
12 runs over 12 samples · mean 42.5 Mbp per run (median 33.0 Mbp, total 0.51 Gbp; 12 runs with a base count) · layout SINGLE 12 · platform LS454 12 · models 454 GS FLX Titanium (12) · 0% of runs with a Sandpiper profile · first public 2014-10-29
Authors (6)
Pérez-Cobas AE first · Artacho A · Ott SJ · Moya A · Gosalbes MJ · Latorre A last
Downloads
PRJEB5771.csv.gz (1.3 KB) · parquet (71.0 KB) — all 12 samples, every field with route and confidence · PRJEB5771_determinations.csv.gz (1.7 KB) — 105 evidence rows