Gut microbiota response to antibiotics in adults, Germany
22 gut metagenome samples from adults in Germany, collected before, during and after antibiotic treatment in an intervention study examining effects on microbiota composition and function. machine-written summary
22 samples · 22 runs · DE · Adult · 2014 · 23.7 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 110 sample values (collection date, country, latitude, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 104 sample values (antibiotic exposure, health condition, health condition detail, location locality, location site) · PMC3839934, PMC4163665 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 single_arm_before_after
longitudinal
5 of 5 people sampled more than once (22 samples; median 5, up to 6 per person) · follow-up median 14 d (max 28 d) · median interval between samples 3 d (time from collection dates). Schedule stated by the source: “Samples before (day 0), during, and after antibiotic treatment; last sample 3-28 days post-treatment depending on patient.” (time origin: treatment start); stated follow-up 28 d.
Each row is one person (5 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 19 | 86% | 19 | |||
| subject_id | 22 | 100% | 22 | |||
| antibiotic_exposure | 22 | 100% | 22 | |||
| collection_date | 22 | 100% | 22 | |||
| detailed_location | 22 | 100% | ||||
| latitude | 22 | 100% | 22 | |||
| location_locality | 22 | 100% | 22 | |||
| location_site | 22 | 100% | 22 | |||
| longitude | 22 | 100% | 22 | |||
| health_condition_detail | 19 | 86% | 19 |
- Differential effects of antibiotic therapy on the structure and function of human gut microbiota. 2013 PMID 24282523 PMC3839934 own_data
- Structural and functional changes in the gut microbiota associated to Clostridium difficile infection. 2014 PMID 25309515 PMC4163665 unsure
Archive description
We performed a metagenomic study to describe the effect of different antibiotics on the gut microbiota of five individuals. We sequenced the metagenomes, metatranscriptomes and the amplicons of the 16SrDNA gene of samples before, during and after the antibiotic treatment for each patient. It was used a Roche GS FLX sequencer and Titanium chemistry for the pyrosequencing.
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.title · “on the human intestinal microbiota”
- body site study.description · “antibiotics on the gut microbiota of five”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA1965846 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.abstract | Four individuals were treated with different antibiotics |
| SAMEA1965846 | collection_date | 2009-08-26 | R1 | 0.90 | biosample.attribute:collection_date | 2009-08-26 |
| SAMEA1965846 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea_region | Germany |
| SAMEA1965846 | health_condition | other_infection | R3 | 0.75 | paper.body.body.Table 1[Pathology] | Erysipelas |
| SAMEA1965846 | health_condition_detail | Erysipelas | R3 | 0.75 | paper.body.body.Table 1[Pathology] | Erysipelas |
| SAMEA1965846 | latitude | 52.5160 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.516 13.4 |
| SAMEA1965846 | location_locality | Kiel | R3 | 0.70 | paper.fulltext.methods | Department of Internal Medicine of the University Hospital Schleswig-Holstein, Campus Kiel |
| SAMEA1965846 | location_site | University Hospital Schleswig-Holstein, Campus Kiel (UK-SH) | R3 | 0.70 | paper.fulltext.methods | Department of Internal Medicine of the University Hospital Schleswig-Holstein |
| SAMEA1965846 | longitude | 13.4000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.516 13.4 |
| SAMEA1965846 | subject_id | B | R1 | 0.70 | sample.name_rule:sample_alias | metagenomeB_after |
Sequencing
22 runs over 22 samples · mean 29.6 Mbp per run (median 23.7 Mbp, total 0.65 Gbp; 22 runs with a base count) · layout SINGLE 22 · platform LS454 22 · models 454 GS FLX Titanium (22) · 0% of runs with a Sandpiper profile · first public 2014-03-31
Authors (9)
Pérez-Cobas AE first · Artacho A · Knecht H · Ferrús ML · Friedrichs A · Ott SJ · Moya A · Latorre A · Gosalbes MJ last
Downloads
PRJEB1389.csv.gz (1.6 KB) · parquet (71.8 KB) — all 22 samples, every field with route and confidence · PRJEB1389_determinations.csv.gz (2.6 KB) — 214 evidence rows