Metagenomes in CDI vs asymptomatic colonization, St. Louis
102 fecal metagenome samples from patients in St. Louis, USA, with C. difficile-associated GI infection or diarrhoea, comparing symptomatic CDI cases to asymptomatically colonized patients in a case-control design. machine-written summary
102 samples · 102 runs · US · Age unknown · 2022 · 1.57 Gbp / sample · cohort Commensal-pathogen dynamics structure disease outc
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 612 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 102 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC8794467, PMC9691601 |
| ○ 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
design observational_with_procedure
Genera, mean relative abundance over 95 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 | 102 | 100% | 102 | |||
| health_condition | 102 | 100% | 102 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 102 | 100% | 102 | |||
| detailed_location | 102 | 100% | ||||
| latitude | 102 | 100% | 102 | |||
| location_locality | 102 | 100% | 102 | |||
| location_region | 102 | 100% | 102 | |||
| longitude | 102 | 100% | 102 |
- Multi-omics investigation of <i>Clostridioides difficile</i>-colonized patients reveals pathogen and commensal correlates of <i>C. difficile</i> pathogenesis. 2022 PMID 35083969 PMC8794467 own_data
- Enterococci enhance Clostridioides difficile pathogenesis. 2022 PMID 36385534 PMC9691601 own_data
- Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. 2025 PMID 39731916 PMC11717617 unsure
Archive description
Shotgun metagenomic sequencing of C. difficile-associated stools
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host study.title · “C. difficile colonized patients”
- body site study.title · “Fecal metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20325554 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN20325554 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: St. Louis |
| SAMN20325554 | health_condition | gi_infection_or_diarrhoea | R4 | 0.50 | study.description | C. difficile-associated stools |
| SAMN20325554 | latitude | 38.6270 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN20325554 | location_locality | St. Louis | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: St. Louis |
| SAMN20325554 | location_region | Missouri | R1 | 0.60 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN20325554 | longitude | -90.1994 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
Sequencing
102 runs over 102 samples · mean 1.98 Gbp per run (median 1.57 Gbp, total 202.45 Gbp; 102 runs with a base count) · layout PAIRED 102 · platform ILLUMINA 102 · models NextSeq 500 (102) · 93% of runs with a Sandpiper profile · first public 2022-01-01
Authors (54)
Fishbein SR first · Robinson JI · Hink T · Reske KA · Newcomer EP · Burnham CD · Henderson JP · Dubberke ER · Dantas G last · Smith AB first · Jenior ML · Keenan O · Hart JL · Specker J · Abbas A · Rangel PC · Di C · Green J · Bustin KA · Gaddy JA · Nicholson MR · Laut C · Kelly BJ · Matthews ML · Evans DR · Van Tyne D · Furth EE · Papin JA · Bushman FD · Erlichman J · Baldassano RN · Silverman MA · Dunny GM · Prentice BM · Skaar EP · Zackular JP last · Fishbein SRS first · DeVeaux AL · Khanna S · Ferreiro AL · Liao J · Agee W · Ning J · Mahmud B · Wallace MJ · Cass C · Guruge J · Leekha S · Rengarajan S · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA748262.csv.gz (3.2 KB) · parquet (73.7 KB) — all 102 samples, every field with route and confidence · PRJNA748262_determinations.csv.gz (4.6 KB) — 714 evidence rows