Antibiotic effects on gut flora in healthy adults, Sweden
547 gut metagenome samples from healthy adult participants in Sweden, in a randomized trial comparing untreated controls to five different antibiotics for urinary tract infection, sampled before and up to one year after treatment. machine-written summary
548 samples · 548 runs · SE · Adult · 2026 · 11.25 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,603 sample values (age, antibiotic exposure, collection date, country, diet, diet detail, intervention, intervention detail) |
| ✓ Abstract / description | 548 sample values (health condition) |
| – Full text | no open-access full text linked |
| – 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 resolved
66 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population healthy_control · Randomized 5-day course: nitrofurantoin, pivmecillinam, sulfamethoxazole/trimethoprim, ceftibuten, ciprofloxacin, or untreated
“randomized to one of 6 treatment arms” — bioproject.description (study level; per-sample arms are in the intervention column below)
antibiotic exposure: two sequence archives disagree for 328 samples (e.g. no vs yes) — withheld.
The sources disagree on 328 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 328)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA120835019 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835020 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835022 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835023 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835025 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835028 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835029 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835031 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835034 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835035 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835036 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835037 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835038 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835040 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835041 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835045 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835048 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835050 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835051 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835052 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835053 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835056 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835057 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835059 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835061 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835062 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835064 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835068 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835070 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835071 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835074 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835075 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835076 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835077 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835079 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835080 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835081 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835086 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835088 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMEA120835089 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
longitudinal
80 of 80 people sampled more than once (548 samples; median 7, up to 8 per person) · follow-up median 12 mo (max 13 mo) · median interval between samples 51 d (time from collection dates). Schedule stated by the source: “Before treatment, then 7, 14, 30, 90 days, 6 months, and 1 year post-treatment” (time origin: treatment start (intervention_date)); stated follow-up 12 mo.
Each row is one person (36 shown of 80); 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 | 548 | 100% | ||||
| country | 548 | 100% | 548 | |||
| health_condition | 548 | 100% | 548 | |||
| subject_id | 548 | 100% | 548 | |||
| age_at_collection_days | 548 | 100% | 548 | |||
| collection_date | 548 | 100% | 548 | |||
| intervention | 548 | 100% | 548 | |||
| sex | 548 | 100% | 548 | |||
| timepoint_label | 548 | 100% | 548 | |||
| detailed_location | 547 | 100% | ||||
| intervention_detail | 547 | 100% | 547 | |||
| latitude | 547 | 100% | 547 | |||
| location_region | 547 | 100% | 547 | |||
| longitude | 547 | 100% | 547 | |||
| antibiotic_exposure | 219 | 40% | 219 | |||
| diet | 180 | 33% | 180 | |||
| diet_detail | 180 | 33% | 180 |
Archive description
This randomized trial evaluated the effect of the use of common antibiotics to treat unrinary tract infections over over a year of follow up. A total of 84 clinically healthy participants with no chronic medication use were enrolled. Participants were randomized to one of 6 treatment arms: untreated, nitrofurantoin, pivmecillinam, sulfamethoxazole/ trimethoprim, ceftibuten, or ciprofloxacin. All antibiotics were given for a five-day course according to standard clinical dosing. Samples were collected before treatment and 7, 14, 30, 90, 6 months, and 1 year post treatment. Samples for sequencing were collected in DNA/RNA shield and frozen at -80 until sequenced. Samples were extracted using bead beating with lysozyme and the Zymo Quick-DNA Magbead Plus kit using a Tecan Freedom EVO robotic system. Samples were sequenced using a 2x100 paired end approach on the DNBSEQ sequencing instruments (MGI, Shenzhen, China). Sequences were demultiplexed using an inhouse demultiplexing algorithm. Sequences were quality-filtered using fastp (v. 0.2.0)12 and human reads were removed using Kraken 2 (v. 2.0.8-beta) by aligning reads against the 38th release of the Human Genome Assembly GRCh38 and retaining only those that did not align with the genome. The study found differing effects on the taxonomic microbiome composition from different antibiotics the mechanism of excretion was related to the impact.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host study.description · “84 clinically healthy participants”
- host study.description · “human reads were removed”
- body site study.title · “normal intestinal flora”
- body site run.scientific_name · “feces metagenome”
- life stage sample.attr.age · “23.0 (n=500/548)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA120835019 | age_at_collection_days | 8391.0 | R1 | 0.85 | sample.attr.age | 23.0 |
| SAMEA120835021 | antibiotic_exposure | yes | R1 | 0.95 | biosample_attr | ceftibuten |
| SAMEA120835019 | collection_date | 2017-10-24 | R1 | 0.90 | biosample.attribute:collection_date | 2017-10-24 |
| SAMEA120835221 | collection_date | 2017-12-01 | R1 | 0.85 | biosample.attribute:collection date | collection date: 2017-12-01 |
| SAMEA120835019 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA120835019 | diet | vegetarian | R1 | 0.85 | biosample.attribute:vegetarian | 1 |
| SAMEA120835019 | diet_detail | vegetarian | R1 | 0.85 | biosample.attribute:vegetarian | 1 |
| SAMEA120835019 | health_condition | healthy_control | R4 | 0.50 | study.description | clinically healthy participants with no chronic medication |
| SAMEA120835019 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:timepoint | timepoint: 0.0 |
| SAMEA120835020 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:days_since_intervention | days_since_intervention: -3.0 |
| SAMEA120835040 | intervention | antibiotic | R1 | 0.90 | biosample.attribute:antibiotic | antibiotic: nitrofurantoin |
| SAMEA120835019 | intervention_detail | timepoint = 0.0 (before intervention start); assigned arm: ciprofloxacin, 5-day course | R1 | 0.80 | biosample.attribute:timepoint | timepoint: 0.0 |
| SAMEA120835020 | intervention_detail | days_since_intervention = -3.0 (before intervention start); assigned arm: pivmecillinam, 5-day course | R1 | 0.80 | biosample.attribute:days_since_intervention | days_since_intervention: -3.0 |
| SAMEA120835040 | intervention_detail | nitrofurantoin, 5-day course | R1 | 0.90 | biosample.attribute:antibiotic | antibiotic: nitrofurantoin |
| SAMEA120835019 | latitude | 59.8580 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.858 17.642 |
| SAMEA120835019 | location_region | Uppsala | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.858 17.642 |
| SAMEA120835019 | longitude | 17.6420 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.858 17.642 |
| SAMEA120835019 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMEA120835019 | subject_id | 1008 | R1 | 0.85 | sample.attr.host_subject_id | 1008 |
| SAMEA120835221 | subject_id | 1053 | R1 | 0.85 | biosample.attribute:host_subject_id | host_subject_id: 1053 |
| SAMEA120835019 | timepoint_label | 0.0 | R1 | 0.85 | sample.attr.days_since_intervention | 0.0 |
| SAMEA120835221 | timepoint_label | 14.0 | R1 | 0.85 | biosample.attribute:days_since_intervention | days_since_intervention: 14.0 |
Sequencing
548 runs over 548 samples · mean 11.37 Gbp per run (median 11.25 Gbp, total 6,231.65 Gbp; 548 runs with a base count) · layout PAIRED 548 · platform DNBSEQ 548 · models DNBSEQ-T7 (548) · 0% of runs with a Sandpiper profile · first public 2026-07-31
Authors (0)
No author record.
Downloads
PRJEB105465.csv.gz (19.8 KB) · parquet (95.4 KB) — all 548 samples, every field with route and confidence · PRJEB105465_determinations.csv.gz (59.9 KB) — 7,151 evidence rows