Gut microbiota resilience after β-lactams in healthy adults
Faecal samples (N=22) from healthy adults in India and France, collected over 90 days following a 3-day course of intravenous β-lactam antibiotics. Longitudinal study of bacterial, phage, and fungal microbiota perturbation and recovery, including metabolome and β-lactamase activity. machine-written summary
22 samples · 22 runs · IN, FR · Adult · 2023 · 25.08 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 | 38 sample values (country, health condition, health condition detail) |
| ✓ Abstract / description | 50 sample values (antibiotic exposure, health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10929231 |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population healthy_control · IV cefotaxime or ceftriaxone for 3 days in healthy volunteers, sampled up to day 90
“treated healthy volunteers either with cefotaxime or ceftriaxone” — abstract:38468305 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “faecal samples collected up to 90 days following a 3-day course of intravenous β-lactam antibiotics” (time origin: intervention_start); stated follow-up 3 mo.
Genera, mean relative abundance over 20 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 22 | 100% | 8 | 14 | ||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 22 | 100% | 22 | |||
| health_condition_detail | 22 | 100% | 8 | 14 |
- 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 unsure
Archive description
Background Antibiotics notoriously perturb the gut microbiota. We used untargeted and targeted phenotypic and genotypic approaches to study faecal samples collected up to 90 days following a 3-day course of intravenous β-lactam antibiotics in 22 healthy volunteers. We studied the changes of the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity of the stools. This allowed to assess their degrees of perturbation and resilience. Results While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, its impact was relatively low on the fungal microbiota. In the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state similar to the initial one, even if the taxonomic composition of the bacterial microbiota changed. However, the dynamics of the different components overtime were rarely correlated. The richness of the resistome was significantly reduced up to day 30, while a significant increase in the relative abundance of β-lactamase encoding genes was observed up to day 10, consistent with concomitant increase in the β-lactamase activity of the microbiota. The level of β-lactamase activity at baseline was associated with the resilience of the metabolome content of the stools.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “faecal samples collected up to 90 days”
- life stage study.description · “22 healthy volunteers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112298745 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days |
| SAMEA112298745 | country | IN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | India |
| SAMEA112486833 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | healthy |
| SAMEA112298745 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy volunteers |
| SAMEA112486833 | health_condition_detail | healthy | R1 | 0.90 | sample.attr.host_health_state | healthy |
| SAMEA112298745 | health_condition_detail | Healthy volunteers with no disease | R4 | 0.50 | paper.abstract | healthy volunteers |
Sequencing
22 runs over 22 samples · mean 23.70 Gbp per run (median 25.08 Gbp, total 521.45 Gbp; 22 runs with a base count) · layout PAIRED 22 · platform ILLUMINA 22 · models Illumina HiSeq 2500 (22) · 91% 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
PRJEB58815.csv.gz (1.4 KB) · parquet (69.6 KB) — all 22 samples, every field with route and confidence · PRJEB58815_determinations.csv.gz (1.2 KB) — 88 evidence rows