Probiotic/antibiotic effects on gut microbiota, Canada
2 fecal samples from healthy adults in London, Ontario, Canada, from a randomized, double-blind, placebo-controlled trial examining probiotic and antibiotic (amoxicillin-clavulanic acid) effects on gut microbiota and resistome. machine-written summary
2 samples · 2 runs · CA · Adult · 2017 · 58.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 14 sample values (collection date, country, latitude, location locality, location region, longitude, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2 sample values (antibiotic exposure) · PMC6060159, PMC6901069 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 4 sample values (health condition, health condition detail) · from GMrepo v3 |
| – 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 Probiotic (live microorganisms; single strain or mixture) design randomized_controlled_trial · population healthy_control · Probiotic (L. rhamnosus/L. helveticus) vs placebo following amoxicillin-clavulanic acid in healthy adults
“probiotic (Lactobacillus rhamnosus R0011 and Lactobacillus helveticus R0052) and placebo groups” — abstract:30046129 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Four fecal samples per participant at one week intervals: baseline (visit 2), antibiotic+probiotic/placebo (visit 3), probiotic/placebo-only (visit 4), wash-out (visit 5)” (time origin: intervention_start); stated follow-up 21 d.
Genera, mean relative abundance over 2 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 | 2 | 100% | ||||
| country | 2 | 100% | 2 | |||
| health_condition | 2 | 100% | 2 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 2 | 100% | 2 | |||
| collection_date | 2 | 100% | 2 | |||
| detailed_location | 2 | 100% | ||||
| health_condition_detail | 2 | 100% | 2 | |||
| latitude | 2 | 100% | 2 | |||
| location_locality | 2 | 100% | 2 | |||
| location_region | 2 | 100% | 2 | |||
| longitude | 2 | 100% | 2 | |||
| timepoint_label | 2 | 100% | 2 |
- Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults. 2018 PMID 30046129 PMC6060159 own_data
- Systematic processing of ribosomal RNA gene amplicon sequencing data. 2019 PMID 31816087 PMC6901069 own_data
Archive description
In this study, we describe a randomized, double-blind and placebo-controlled clinical trial done with a cohort of 70 individuals at 4 different time points in the objective of evaluatinged the impact of a probiotic combination following administration of antibiotic in 70 healthy adults.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host study.title · “human gut metagenome”
- body site study.title · “human gut metagenome”
- life stage study.description · “70 healthy adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07795010 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.methods | received 1 capsule per day of the antimicrobial |
| SAMN07795010 | collection_date | 2014-05 | R1 | 0.90 | biosample.attribute:collection_date | 2014-05 |
| SAMN07795010 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada:Ontario,London |
| SAMN07795010 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07795010 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07795010 | latitude | 42.5000 | R1 | 0.90 | biosample.attribute:lat_lon | 42.5 N 81.26 W |
| SAMN07795010 | location_locality | London | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada:Ontario,London |
| SAMN07795010 | location_region | Ontario | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada:Ontario,London |
| SAMN07795010 | longitude | -81.2600 | R1 | 0.90 | biosample.attribute:lat_lon | 42.5 N 81.26 W |
| SAMN07795010 | timepoint_label | v3 | R1 | 0.85 | sample.attr.visit | v3 |
Sequencing
2 runs over 2 samples · mean 58.30 Gbp per run (median 58.30 Gbp, total 116.60 Gbp; 2 runs with a base count) · layout PAIRED 2 · platform ILLUMINA 2 · models Illumina HiSeq 2500 (2) · 100% of runs with a Sandpiper profile · first public 2017-10-19 – 2017-10-20
Authors (8)
MacPherson CW first · Mathieu O · Tremblay J · Champagne J · Nantel A · Girard SA · Tompkins TA last · Yergeau E last
Downloads
PRJNA414540.csv.gz (959 B) · parquet (70.1 KB) — all 2 samples, every field with route and confidence · PRJNA414540_determinations.csv.gz (945 B) — 20 evidence rows