C. difficile colonization in adults, St. Louis fecal metagenomes
86 fecal metagenome samples from adults in St. Louis, USA, including C. difficile carriers, other infections, and healthy controls, studied alongside gnotobiotic mouse models of C. difficile colonization and infection. machine-written summary
86 samples · 437 runs · US · Adult · 2025 · 1.42 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 | 688 sample values (collection date, country, health condition, latitude, location locality, location region, longitude, subject id) |
| ✓ Abstract / description | 86 sample values (health condition detail) |
| ✓ Full text | 86 sample values (location site) · PMC11717617 |
| – 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 not resolved
design observational_with_procedure
longitudinal
13 of 65 people sampled more than once (34 samples; median 2, up to 7 per person) · follow-up median 12 d (max 3 mo) · median interval between samples 7 d (time from collection dates).
Each row is one person (13 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 437 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 | 86 | 100% | ||||
| country | 86 | 100% | 86 | |||
| health_condition | 86 | 100% | 86 | |||
| subject_id | 86 | 100% | 86 | |||
| collection_date | 86 | 100% | 86 | |||
| detailed_location | 86 | 100% | ||||
| health_condition_detail | 86 | 100% | 86 | |||
| latitude | 86 | 100% | 86 | |||
| location_locality | 86 | 100% | 86 | |||
| location_region | 86 | 100% | 86 | |||
| location_site | 86 | 100% | 86 | |||
| longitude | 86 | 100% | 86 |
- Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. 2025 PMID 39731916 PMC11717617 own_data
Archive description
Shotgun metagenomics sequencing data from adults colonized with C. difficile and gnotobiotic animal models of C. difficile colonization and infection
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host study.title · “mouse and human fecal metagenomes”
- host run.host_tax_id · “10090”
- body site study.title · “fecal metagenomes”
- life stage study.description · “adults colonized with C. difficile”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39571805 | collection_date | 2019-03-10 | R1 | 0.90 | biosample.attribute:collection_date | 2019-03-10 |
| SAMN39571805 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: St. Louis |
| SAMN39571805 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | CDI |
| SAMN39571805 | health_condition_detail | Clostridioides difficile colonization | R4 | 0.50 | study.description | adults colonized with C. difficile |
| SAMN39571805 | latitude | 38.6270 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN39571805 | location_locality | St. Louis | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: St. Louis |
| SAMN39571805 | location_region | Missouri | R1 | 0.60 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN39571805 | location_site | Barnes-Jewish Hospital | R3 | 0.70 | paper.fulltext.methods | Barnes-Jewish Hospital (BJH) in St. Louis, MO, USA |
| SAMN39571805 | longitude | -90.1994 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN39571805 | subject_id | CNTM_P59 | R1 | 0.85 | sample.attr.participant_id | CNTM_P59 |
Sequencing
437 runs over 86 samples · mean 1.62 Gbp per run (median 1.42 Gbp, total 706.73 Gbp; 437 runs with a base count) · layout PAIRED 437 · platform ILLUMINA 437 · models Illumina NovaSeq 6000 (259), NextSeq 550 (160), Illumina NovaSeq X Plus (18) · 100% of runs with a Sandpiper profile · first public 2025-03-02 – 2025-04-17
Authors (17)
Fishbein SRS first · DeVeaux AL · Khanna S · Ferreiro AL · Liao J · Agee W · Ning J · Mahmud B · Wallace MJ · Hink T · Reske KA · Cass C · Guruge J · Leekha S · Rengarajan S · Dubberke ER · Dantas G last
Downloads
PRJNA1067813.csv.gz (3.6 KB) · parquet (75.1 KB) — all 86 samples, every field with route and confidence · PRJNA1067813_determinations.csv.gz (6.9 KB) — 860 evidence rows