Rib fracture trauma patients vs controls, Nottingham, UK
662 gut metagenome samples from a case-control study in Nottingham, UK, comparing hospitalized multiple rib fracture trauma patients to age- and sex-matched controls, examining antibiotic treatment effects on microbiome and AMR genes. machine-written summary
662 samples · 662 runs · GB · Age unknown · 2024 · 8.07 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,136 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 662 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11403444 |
| ○ 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 · share metadata |
| – 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 observational_with_procedure · population other_disease · Clinical antibiotic treatment in trauma patients, observed pre/post
“antibiotic-treated and untreated patients” — abstract:39286492 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
238 of 344 people sampled more than once (476 samples; median 2, up to 2 per person). Schedule stated by the source: “Samples at hospital discharge, then 6 weeks and 12 weeks post-discharge follow-up” (time origin: other:discharge); stated follow-up 3 mo.
Genera, mean relative abundance over 638 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 | 662 | 100% | 662 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 582 | 88% | 582 | |||
| collection_date | 662 | 100% | 662 | |||
| detailed_location | 662 | 100% | ||||
| health_condition_detail | 662 | 100% | 662 | |||
| latitude | 662 | 100% | 662 | |||
| location_locality | 662 | 100% | 662 | |||
| location_region | 662 | 100% | 662 | |||
| longitude | 662 | 100% | 662 | |||
| timepoint_label | 582 | 88% | 582 |
- Metagenomic changes in response to antibiotic treatment in severe orthopedic trauma patients. 2024 PMID 39286492 PMC11403444 own_data
Archive description
Metagenomic samples form cases (rib fracture trauma patients) and controls from various exercise and diet intervention studies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host study.title · “Metagenomics of rib fracture cases and controls”
- body site sample.attr.isolation_source · “Gut (n=662/662)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN41320825 | collection_date | 2023-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2023-01-01 |
| SAMN41320825 | country | GB | R1 | 0.90 | sample.attr.geo_loc_name | United Kingdom: Nottingham |
| SAMN41320825 | health_condition_detail | mixed_case_control: Cases: severe orthopedic trauma (rib fracture) patients; Controls: age- and sex-matched controls fro | R4 | 0.50 | paper.abstract | 16 hospitalized multiple rib fractures patients and 10 age- and sex-matched controls |
| SAMN41320825 | latitude | 52.9536 | R1 | 0.90 | biosample.attribute:lat_lon | 52.9536 N 1.15047 W |
| SAMN41320825 | location_locality | Nottingham | R1 | 0.85 | biosample.attribute:geo_loc_name | United Kingdom: Nottingham |
| SAMN41320825 | location_region | England | R1 | 0.60 | biosample.attribute:lat_lon | 52.9536 N 1.15047 W |
| SAMN41320825 | longitude | -1.1505 | R1 | 0.90 | biosample.attribute:lat_lon | 52.9536 N 1.15047 W |
| SAMN41320876 | subject_id | 01832 | R1 | 0.70 | sample.name_rule:library_names | 01832_V1 |
| SAMN41320876 | timepoint_label | V1 | R1 | 0.70 | sample.name_rule:library_names | 01832_V1 |
Sequencing
662 runs over 662 samples · mean 9.05 Gbp per run (median 8.07 Gbp, total 5,989.11 Gbp; 662 runs with a base count) · layout PAIRED 662 · platform ILLUMINA 662 · models Illumina NovaSeq X Plus (514), Illumina NovaSeq 6000 (148) · 96% of runs with a Sandpiper profile · first public 2024-05-12 – 2026-03-04
Authors (14)
Kouraki A first · Zheng AS · Miller S · Kelly A · Ashraf W · Bazzani D · Bonadiman A · Tonidandel G · Bolzan M · Vijay A · Nightingale J · Menni C · Ollivere BJ · Valdes AM last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1110178.csv.gz (18.0 KB) · parquet (95.8 KB) — all 662 samples, every field with route and confidence · PRJNA1110178_determinations.csv.gz (43.8 KB) — 5,798 evidence rows