Gut microbiome in healthy adults given beta-lactams, Rennes
335 fecal/plasma samples from healthy adult volunteers in Rennes, France, in a randomized controlled intervention study comparing gut microbiome impact of IV beta-lactam antibiotics (ceftriaxone, piperacillin/tazobactam, ceftazidime/avibactam), with or without the DAV132 adsorbent. machine-written summary
335 samples · 335 runs · FR · Adult · 2024 · 6.49 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 4,427 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, intervention) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 299 sample values (health condition detail) · PMC11402973, PMC12931723 |
| ○ 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 |
longitudinal
119 of 119 people sampled more than once (335 samples; median 3, up to 3 per person) · follow-up median 36 d (max 36 d) · median interval between samples 31 d (time from timepoint labels). Schedule stated by the source: “Stool collected before treatment, daily day1-9, and at days 12,16,25,37; BioSample timepoints Day1, Day6, Day37” (time origin: intervention_start); stated follow-up 37 d.
Each row is one person (36 shown of 119); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 304 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 | 335 | 100% | ||||
| country | 335 | 100% | 335 | |||
| health_condition | 335 | 100% | 335 | |||
| subject_id | 335 | 100% | 335 | |||
| age_at_collection_days | 335 | 100% | 335 | |||
| bmi | 335 | 100% | 335 | |||
| collection_date | 335 | 100% | 335 | |||
| detailed_location | 335 | 100% | ||||
| health_condition_detail | 335 | 100% | 36 | 299 | ||
| intervention | 335 | 100% | 335 | |||
| intervention_detail | 335 | 100% | 335 | |||
| latitude | 335 | 100% | 335 | |||
| location_locality | 335 | 100% | 335 | |||
| longitude | 335 | 100% | 335 | |||
| sex | 335 | 100% | 335 | |||
| timepoint_label | 335 | 100% | 335 | |||
| antibiotic_exposure | 36 | 11% | 36 |
- The DAV132 colon-targeted adsorbent does not interfere with plasma concentrations of antibiotics but prevents antibiotic-related dysbiosis: a randomized phase I trial in healthy volunteers. 2024 PMID 39278946 PMC11402973 own_data
- A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity. 2025 PMID 39711113 PMC12931723 own_data
- Antibiotic-related dysbiosis of gut microbiota in healthy volunteers: a comparative study of ceftazidime-avibactam, piperacillin-tazobactam, and ceftriaxone. 2025 PMID 40504338 own_data
Archive description
The main purpose of this randomized, open-label, parallel groups, controlled study was to assess in healthy volunteers the performance of DAV132, a class IIa medical device, in capturing by adsorption the aforementioned beta-lactams in the large intestine without impacting the antimicrobial efficacy. DAV132, a charcoal-based adsorbent, was given at 7.5 g or 12 g tid orally for 7 days to healthy volunteers treated with ceftriaxone 1 g oad, or piperacillin/tazobactam 4 g/0.5 g q8h, or ceftazidime/avibactam 2 g/0.5 g q8h, intravenously for 5 days, comparatively to subjects only receiving the same beta-lactam treatment or no treatment at all. Evaluation of the impact of the presence of antibiotics residuals in the large intestine on intestinal microbiome was performed with shotgun metagenomic at baseline, just after the end of antibiotic treatments and one month after end of treatments.
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_unknown_no_evidence”
- body site study.title · “beta-lactam antibiotics on intestinal microbiome of human”
- body site study.description · “in the large intestine without impacting the”
- life stage study.title · “of human healthy volunteers and protection with”
- life stage study.description · “assess in healthy volunteers the performance of”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33739980 | age_at_collection_days | 20088.8 | R1 | 0.70 | sample.attr.host_age | 55 |
| SAMN33739985 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:host_group | host_group: Ct Group: Control - No treatment |
| SAMN33739980 | bmi | 23.06 | R1 | 0.90 | sample.attr.host_body_mass_index | 23.06 |
| SAMN33739980 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN33739980 | country | FR | R1 | 0.90 | sample.attr.geo_loc_name | France: Rennes |
| SAMN33739980 | health_condition | intervention_cohort | R1 | 0.90 | biosample_attr | CROD1 Group: ceftriaxone (1 g oad i.v.) + DAV132 7.5 g tid |
| SAMN33739985 | health_condition_detail | Ct Group: Control - No treatment | R1 | 0.85 | biosample.attribute:host_group | host_group: Ct Group: Control - No treatment |
| SAMN33739980 | health_condition_detail | healthy volunteers | R3 | 0.70 | paper.fulltext.abstract | 148 healthy volunteers (HV) to test two doses |
| SAMN33739980 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:host_timepoint | host_timepoint: Day1 |
| SAMN33739981 | intervention | antibiotic;other_intervention | R1 | 0.80 | biosample.attribute:host_group | host_group: CROD1 Group: ceftriaxone (1 g oad i.v.) + DAV132 7.5 g |
| SAMN33739980 | intervention_detail | baseline before antibiotic dosing; assigned arm: ceftriaxone IV + DAV132 7.5g tid adsorbent | R1 | 0.80 | biosample.attribute:host_timepoint | host_timepoint: Day1 |
| SAMN33739981 | intervention_detail | ceftriaxone IV + DAV132 7.5g tid adsorbent | R1 | 0.80 | biosample.attribute:host_group | host_group: CROD1 Group: ceftriaxone (1 g oad i.v.) + DAV132 7.5 g |
| SAMN33739980 | latitude | 48.7000 | R1 | 0.90 | biosample.attribute:lat_lon | 48.7 N 1.4 W |
| SAMN33739980 | location_locality | Rennes | R1 | 0.85 | biosample.attribute:geo_loc_name | France: Rennes |
| SAMN33739980 | longitude | -1.4000 | R1 | 0.90 | biosample.attribute:lat_lon | 48.7 N 1.4 W |
| SAMN33739980 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN33739980 | subject_id | 0002 | R1 | 0.85 | sample.attr.host_subject_id | 0002 |
| SAMN33739980 | timepoint_label | Day1 | R1 | 0.85 | sample.attr.host_timepoint | Day1 |
Sequencing
335 runs over 335 samples · mean 6.52 Gbp per run (median 6.49 Gbp, total 2,183.74 Gbp; 335 runs with a base count) · layout PAIRED 335 · platform ILLUMINA 335 · models Illumina NovaSeq 6000 (335) · 91% of runs with a Sandpiper profile · first public 2024-02-03 – 2024-02-25
Authors (29)
Messaoudene M first · Ferreira S · Saint-Lu N · Ponce M · Truntzer C · Boidot R · Le Bescop C · Loppinet T · Corbel T · Féger C · Bertrand K · Elkrief A · Isaksen M · Vitry F · Sablier-Gallis F · Andremont A · Bod L · Ghiringhelli F · de Gunzburg J · Routy B last · Olivares C first · Ruppé E · Guedj J · Burdet C last · Huang G first · Cai L · Guo J · Zhu R · Zhu L last
Downloads
PRJNA922086.csv.gz (11.0 KB) · parquet (85.9 KB) — all 335 samples, every field with route and confidence · PRJNA922086_determinations.csv.gz (35.6 KB) — 4,726 evidence rows