DFI C. difficile Gut Metagenomics Profiling
73 gut metagenome samples profiled in relation to C. difficile; no further details on population, location, or design are provided in the available records. machine-written summary
73 samples · 73 runs · US · Age unknown · 2026 · 1.81 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 146 sample values (collection date, country) |
| ✓ Abstract / description | 73 sample values (location site) |
| – Full text | no open-access full text linked |
| – 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 73 | 100% | 73 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 73 | 100% | 73 | |||
| detailed_location | 73 | 100% | ||||
| location_site | 73 | 100% | 73 |
Archive description
Clostridium difficile (C. difficile), the leading cause of healthcare-associated diarrhea, is a spore-forming obligate anaerobe that colonizes the intestinal tract and causes colitis in patients with compromised microbiome- mediated defenses. C. difficile is genomically diverse and strains can be classified into sequence type (ST)s that vary in virulence and epidemic potential. Since secretion of the TcdB exotoxin is common to nearly all disease-associated C. difficile strains, PCR detection of TcdB is the principal clinical test used to diagnose</p><p>C. difficile infection (CDI). This test, however, cannot distinguish between strains and thus is unable to determine the prevalence of different C. difficile STs in healthcare settings. Traditional strain typing methods require anaerobic fecal culturing to isolate C. difficile, but is technically demanding and time consuming and thus is rarely used to distinguish sporadic from epidemic occurrences of CDI. To address this, we have optimized strain-level profiling of fecal metagenomic sequence data and demonstrate the potential for fecal nucleic acid sequencing to support epidemiologic surveillance of C. difficile in healthcare environments.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host study.description · “colonizes the intestinal tract and causes colitis in patients”
- body site study.description · “fecal nucleic acid sequencing to support epidemiologic surveillance”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47983614 | collection_date | 2020-11-06 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2020-11-06 |
| SAMN47983614 | country | US | R1 | 0.85 | biosample.attribute:geo_loc_name | geo_loc_name: USA: Chicago, IL |
| SAMN47983614 | location_site | healthcare settings | R4 | 0.45 | ena.study_description | support epidemiologic surveillance of C. difficile in healthcare environments |
Sequencing
73 runs over 73 samples · mean 2.02 Gbp per run (median 1.81 Gbp, total 147.32 Gbp; 73 runs with a base count) · layout PAIRED 73 · platform ILLUMINA 73 · models NextSeq 1000 (73) · 0% of runs with a Sandpiper profile · first public 2026-09-01
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA1251023.csv.gz (2.8 KB) · parquet (72.4 KB) — all 73 samples, every field with route and confidence · PRJNA1251023_determinations.csv.gz (2.4 KB) — 219 evidence rows