Gut microbiome and C. difficile toxin status, USA
Case-control study of 172 stool samples from GDH-positive, C. difficile-colonized patients (mostly elderly and adult) in the USA, examining gut microbiome relationships to toxin gene presence and toxin expression. machine-written summary
172 samples · 172 runs · US · Adult · 2025 · 8.50 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,032 sample values (age, collection date, country, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 344 sample values (location region, subject id) · PMC12570482 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 154 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 | 172 | 100% | ||||
| country | 172 | 100% | 172 | |||
| health_condition | 172 | 100% | 172 | |||
| subject_id | 172 | 100% | 172 | |||
| age_at_collection_days | 172 | 100% | 172 | |||
| collection_date | 172 | 100% | 172 | |||
| detailed_location | 172 | 100% | ||||
| health_condition_detail | 172 | 100% | 172 | |||
| location_region | 172 | 100% | 172 | |||
| sex | 172 | 100% | 172 |
- Microbiome signatures of <i>Clostridioides difficile</i> toxin production and toxin gene presence: a shotgun metagenomic approach. 2025 PMID 40996044 PMC12570482 own_data
Archive description
These data are from a microbiome analysis of stool samples from patients with a range of Clostridiodes difficile-related disease manifestations. All patients were colonized or infected with C. difficile as determined by the presence of the GDH gene. Patients with C. difficile were divided into three toxin groups based the presence or absence of toxin-encoding genes and, if present, whether the toxin genes were expressed. DNA was extracted from stool samples and the DNA was subjected to shotgun metagenomic sequencing on the Illumina NovaSeq. These data were then used to examine relationships between the gut microbiota, individual risk factors, C. difficile recurrence status, and expression of C. difficile genes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Relationships between the gastrointestinal microbiome and Clostridiodes”
- body site study.description · “microbiome analysis of stool samples from patients”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “68 (n=82/172)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39680485 | age_at_collection_days | 25550.0 | R1 | 0.85 | sample.attr.host_age | 70 |
| SAMN39680485 | collection_date | 2019-04 | R1 | 0.90 | biosample.attribute:collection_date | 2019-04 |
| SAMN39680485 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN39680485 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | C.difficile infection |
| SAMN39680485 | health_condition_detail | C.difficile infection | R1 | 0.90 | sample.attr.host_disease | C.difficile infection |
| SAMN39680485 | location_region | Connecticut | R3 | 0.70 | paper.fulltext.methods | Connecticut’s Emerging Infections Program, which conducts C. difficile surveillance in Connecticut |
| SAMN39680485 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN39680485 | subject_id | SAMN39680485 | R3 | 0.75 | design.one_sample_per_subject:fulltext | The stool samples were collected at a single point in time, limiting our ability to |
Sequencing
172 runs over 172 samples · mean 8.36 Gbp per run (median 8.50 Gbp, total 1,437.18 Gbp; 172 runs with a base count) · layout PAIRED 172 · platform ILLUMINA 172 · models Illumina NovaSeq 6000 (172) · 90% of runs with a Sandpiper profile · first public 2025-07-27
Authors (7)
Kwon J first · Correa MA · Kong Y · Pelletiers W · Wade M · Olson D · Pettigrew MM last
Downloads
PRJNA1056768.csv.gz (6.3 KB) · parquet (78.7 KB) — all 172 samples, every field with route and confidence · PRJNA1056768_determinations.csv.gz (9.1 KB) — 1,376 evidence rows