Shotgun metagenomics vs PCR for gastroenteritis, Trondheim
Cross-sectional study of 55 samples (clinical faecal, spiked, and control) from Trondheim, Norway, comparing shotgun metagenomics to PCR for detecting gastrointestinal pathogens in infectious gastroenteritis. machine-written summary
55 samples · 55 runs · NO · Age unknown · 2025 · 6.75 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 400 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12404398 |
| ○ 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 |
longitudinal — not resolved
4 of 4 people sampled more than once (40 samples; median 10, up to 10 per person). Schedule stated by the source: “Single faecal collection per donor/patient; BP sample codes reflect spiking dilution (1/3/5=10^-1,10^-3,10^-5) and replicate letter (a/b/c), not repeat time points.”.
Genera, mean relative abundance over 51 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 | 55 | 100% | 55 | |||
| health_condition | 15 | 27% | 15 | |||
| subject_id | 40 | 73% | 40 | |||
| collection_date | 55 | 100% | 55 | |||
| detailed_location | 55 | 100% | ||||
| latitude | 55 | 100% | 55 | |||
| location_locality | 55 | 100% | 55 | |||
| location_region | 55 | 100% | 55 | |||
| longitude | 55 | 100% | 55 | |||
| health_condition_detail | 15 | 27% | 15 |
- Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis. 2025 PMID 40892803 PMC12404398 own_data
Archive description
In this study, we evaluated metagenomics shotgun sequencing in comparison to PCR as a diagnostic tool for detecting gastrointestinal pathogens in a clinical hospital laboratory. We sequenced a total of 55 samples, including clinical faecal samples, spiked faecal samples, and control samples, and tested various bioinformatics approaches for pathogen and virulence gene detection.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site study.description · “clinical faecal samples, spiked faecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN46532326 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN46532326 | country | NO | R1 | 0.90 | sample.attr.geo_loc_name | Norway: Trondheim |
| SAMN46532326 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:description | human gut metagenome clinical sample |
| SAMN46532326 | health_condition_detail | human gut metagenome clinical sample | R1 | 0.85 | biosample.attribute:description | human gut metagenome clinical sample |
| SAMN46532326 | latitude | 63.4300 | R1 | 0.90 | biosample.attribute:lat_lon | 63.43 N 10.39 E |
| SAMN46532326 | location_locality | Trondheim | R1 | 0.85 | biosample.attribute:geo_loc_name | Norway: Trondheim |
| SAMN46532326 | location_region | Sor-Trondelag | R1 | 0.60 | biosample.attribute:lat_lon | 63.43 N 10.39 E |
| SAMN46532326 | longitude | 10.3900 | R1 | 0.90 | biosample.attribute:lat_lon | 63.43 N 10.39 E |
| SAMN46532341 | subject_id | BP1 | R1 | 0.70 | sample.name_rule:alias | BP1_1a |
Sequencing
55 runs over 55 samples · mean 6.67 Gbp per run (median 6.75 Gbp, total 366.79 Gbp; 55 runs with a base count) · layout PAIRED 55 · platform ILLUMINA 55 · models NextSeq 550 (55) · 93% of runs with a Sandpiper profile · first public 2025-08-21
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1218764.csv.gz (2.3 KB) · parquet (72.0 KB) — all 55 samples, every field with route and confidence · PRJNA1218764_determinations.csv.gz (3.3 KB) — 400 evidence rows