Antibiotic effects on gut microbiome in stool donors
61 longitudinal stool samples from healthy stool donors in Canada (Alberta) and Finland (Helsinki), studying how recent antibiotic use affects gut bacterial diversity, viral populations, and antibiotic resistance genes. machine-written summary
61 samples · 61 runs · CA, FI · Age unknown · 2025 · 3.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 393 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 122 sample values (health condition, health condition detail) · PMC12098650 |
| ○ 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
3 of 3 people sampled more than once (61 samples; median 19, up to 34 per person) · follow-up median 17 mo (max 2.6 y) · median interval between samples 12 d (time from collection dates). Schedule stated by the source: “Donor 1: 34 samples over 31 months; Donor 2: 19 samples over 19 months; Donor 3: 8 samples over 13 months, around antibiotic exposures.”.
Each row is one person (3 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 57 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 | 0 | 0% | ||||
| country | 61 | 100% | 61 | |||
| health_condition | 61 | 100% | 61 | |||
| subject_id | 61 | 100% | 61 | |||
| collection_date | 61 | 100% | 61 | |||
| detailed_location | 61 | 100% | ||||
| health_condition_detail | 61 | 100% | 61 | |||
| latitude | 61 | 100% | 61 | |||
| location_region | 61 | 100% | 61 | |||
| longitude | 61 | 100% | 61 | |||
| location_locality | 27 | 44% | 27 |
- Prolonged effect of antibiotic therapy on the gut microbiota composition, functionality, and antibiotic resistance genes' profiles in healthy stool donors. 2025 PMID 40415928 PMC12098650 own_data
Archive description
This dataset supports a study investigating the effects of recent antibiotic use on gut microbiota recovery in stool donors from Canada and Finland. Using longitudinal stool sampling and metagenomic sequencing, the research explores the lasting disruptions antibiotics cause to bacterial diversity, community composition, microbial functions, viral populations, and antibiotic resistant genes in donors.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “longitudinal stool sampling”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN45963671 | collection_date | 2021-01-15 | R1 | 0.90 | biosample.attribute:collection_date | 2021-01-15 |
| SAMN45963671 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Alberta |
| SAMN45963671 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.abstract | long-term stool donors from Canada and Finland |
| SAMN45963671 | health_condition_detail | healthy stool donors (FMT donors) with recent antibiotic use | R3 | 0.70 | paper.fulltext.abstract | long-term stool donors from Canada and Finland |
| SAMN45963671 | latitude | 53.5216 | R1 | 0.90 | biosample.attribute:lat_lon | 53.5216 N 113.5225 W |
| SAMN45963699 | location_locality | Helsinki | R1 | 0.85 | biosample.attribute:geo_loc_name | Finland: Helsinki |
| SAMN45963671 | location_region | Alberta | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Alberta |
| SAMN45963699 | location_region | Uusimaa | R1 | 0.60 | biosample.attribute:lat_lon | 60.1699 N 24.9384 E |
| SAMN45963671 | longitude | -113.5225 | R1 | 0.90 | biosample.attribute:lat_lon | 53.5216 N 113.5225 W |
| SAMN45963671 | subject_id | 1 | R1 | 0.85 | sample.attr.donor_id | 1 |
Sequencing
61 runs over 61 samples · mean 3.21 Gbp per run (median 3.15 Gbp, total 196.09 Gbp; 61 runs with a base count) · layout PAIRED 61 · platform ILLUMINA 61 · models Illumina NovaSeq 6000 (61) · 93% of runs with a Sandpiper profile · first public 2025-01-29
Authors (6)
Karimianghadim R first · Satokari R · Yeo S · Arkkila P · Kao D · Pakpour S last
Downloads
PRJNA1202717.csv.gz (2.7 KB) · parquet (72.8 KB) — all 61 samples, every field with route and confidence · PRJNA1202717_determinations.csv.gz (4.2 KB) — 515 evidence rows