Gut microbiome resilience after β-lactams, healthy adults
277 faecal samples from healthy adult volunteers in France, collected over 90 days following a 3-day course of cefotaxime or ceftriaxone, in an intervention study of antibiotic-induced microbiome perturbation and recovery. machine-written summary
277 samples · 2,102 runs · FR · Adult · 2023 · 3.04 Gbp / sample · cohort Perturbation and resilience of the gut microbiome
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,662 sample values (country, health condition, intervention, intervention detail, subject id, timepoint) |
| ✓ Abstract / description | 277 sample values (health condition detail) |
| ✓ Full text | 554 sample values (location locality, location site) · PMC10929231 |
| ○ 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 resolved
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population healthy_control · Healthy volunteers treated with cefotaxime or ceftriaxone for 3 days
“treated healthy volunteers either with cefotaxime or ceftriaxone” — abstract:38468305 (study level; per-sample arms are in the intervention column below)
longitudinal
22 of 22 people sampled more than once (277 samples; median 13, up to 13 per person) · follow-up median 6 mo (max 8 mo) · median interval between samples 5 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “stool at days -14, -6, 0, 1, 2, 4, 7, 10, 15 and 30 (up to day 90) per subject” (time origin: intervention_start); stated follow-up 3 mo.
Each row is one person (22 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 | 277 | 100% | ||||
| country | 277 | 100% | 277 | |||
| health_condition | 277 | 100% | 277 | |||
| subject_id | 277 | 100% | 277 | |||
| detailed_location | 277 | 100% | ||||
| health_condition_detail | 277 | 100% | 277 | |||
| intervention | 277 | 100% | 277 | |||
| intervention_detail | 277 | 100% | 277 | |||
| location_locality | 277 | 100% | 277 | |||
| location_site | 277 | 100% | 277 | |||
| timepoint_label | 277 | 100% | 277 |
- Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases. 2024 PMID 38468305 PMC10929231 own_data
Archive description
Perturbation and resilience of the gut microbiome three months after β-lactams exposure in healthy volunteers suggest an important role of endogenous β-lactamases
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 · “resilience of the gut microbiome three months”
- body site study.description · “resilience of the gut microbiome three months”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.title · “exposure in healthy volunteers suggest an important”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112205902 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA112205902 | health_condition | healthy_control | R1 | 0.70 | biosample_attr | ceftriaxone |
| SAMEA112205902 | health_condition_detail | All subjects were healthy volunteers | R4 | 0.50 | paper.abstract | healthy volunteers either with cefotaxime or ceftriaxone |
| SAMEA112205902 | intervention | antibiotic | R1 | 0.90 | biosample.attribute:group | group: ceftriaxone |
| SAMEA112205902 | intervention_detail | ceftriaxone administered | R1 | 0.90 | biosample.attribute:group | group: ceftriaxone |
| SAMEA112205902 | location_locality | Paris | R3 | 0.70 | paper.fulltext.methods | Bichat-Claude Bernard Hospital (Paris, France) |
| SAMEA112205902 | location_site | Clinical Investigation Center of the Bichat-Claude Bernard Hospital | R3 | 0.70 | paper.fulltext.methods | Clinical Investigation Center of the Bichat-Claude Bernard Hospital |
| SAMEA112205902 | subject_id | 1 | R1 | 0.85 | sample.attr.individual | 1 |
| SAMEA112205902 | timepoint_label | 1 | R1 | 0.85 | sample.attr.time | 1 |
Sequencing
2,102 runs over 277 samples · mean 0.41 Gbp per run (median 0.28 Gbp, total 851.79 Gbp; 2,102 runs with a base count) · layout SINGLE 2,102 · platform ION_TORRENT 2,102 · models Ion Torrent Proton (2,102) · 0% of runs with a Sandpiper profile · first public 2023-04-13
Authors (35)
d'Humières C first · Delavy M · Alla L · Ichou F · Gauliard E · Ghozlane A · Levenez F · Galleron N · Quinquis B · Pons N · Mullaert J · Bridier-Nahmias A · Condamine B · Touchon M · Rainteau D · Lamazière A · Lesnik P · Ponnaiah M · Lhomme M · Sertour N · Devente S · Docquier JD · Bougnoux ME · Tenaillon O · Magnan M · Ruppé E · Grall N · Duval X · Ehrlich D · Mentré F · Denamur E · Rocha EPC · Le Chatelier E · Burdet C · PrediRes study group last
Downloads
PRJEB58157.csv.gz (8.5 KB) · parquet (80.3 KB) — all 277 samples, every field with route and confidence · PRJEB58157_determinations.csv.gz (14.6 KB) — 2,493 evidence rows