Gut metagenomics in rCDI and cirrhosis case-control study
66 fecal metagenomic samples from adult and elderly subjects, using proximity-ligation (Hi-C) shotgun metagenomics to compare bacterial host-mobilome ARG and virulence gene links in recurrent C. difficile infection and cirrhosis cohorts versus healthy controls, case-control design. machine-written summary
66 samples · 66 runs · US · Adult · 2026 · 39.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 396 sample values (country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 66 sample values (subject id) · PMC13524746 |
| ✓ Supplementary tables | 106 sample values (age, sex) |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 66 | 100% | ||||
| country | 66 | 100% | 66 | |||
| health_condition | 66 | 100% | 66 | |||
| subject_id | 66 | 100% | 66 | |||
| detailed_location | 66 | 100% | ||||
| health_condition_detail | 66 | 100% | 66 | |||
| latitude | 66 | 100% | 66 | |||
| location_region | 66 | 100% | 66 | |||
| longitude | 66 | 100% | 66 | |||
| age_at_collection_days | 53 | 80% | 53 | |||
| sex | 53 | 80% | 53 |
- Proximity-ligation metagenomics reveals differential plasmid and chromosomal antimicrobial resistance gene carriage in disrupted gut ecosystems. 2026 PMID 42668680 PMC13524746 own_data
Archive description
Paired-end shotgun metagenomic and Hi-C sequence reads from human fecal samples
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult 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.description · “reads from human fecal samples”
- body site external_curation.infant_catalog · “body_site_call stool”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN57202984 | age_at_collection_days | 29950 | R2 | 0.80 | paper.supp.mmc2.xlsx[Table S1!Age] | 82 |
| SAMN57202984 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Minnesota |
| SAMN57202984 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: Metagenomic reads from rCDI patient feces |
| SAMN57202984 | health_condition_detail | Metagenomic reads from rCDI patient feces | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: Metagenomic reads from rCDI patient feces |
| SAMN57202984 | latitude | 44.9723 | R1 | 0.90 | biosample.attribute:lat_lon | 44.9723 N 93.2335 W |
| SAMN57202984 | location_region | Minnesota | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Minnesota |
| SAMN57202984 | longitude | -93.2335 | R1 | 0.90 | biosample.attribute:lat_lon | 44.9723 N 93.2335 W |
| SAMN57202984 | sex | male | R2 | 0.80 | paper.supp.mmc2.xlsx[Table S1!Sex] | M |
| SAMN57202984 | subject_id | SAMN57202984 | R3 | 0.70 | design.one_sample_per_subject:fulltext | PLSM sequencing was performed on a total of 66 stool samples (19 cirrhosis, 34 rCDI, and 13 healthy individuals) |
Sequencing
66 runs over 66 samples · mean 43.44 Gbp per run (median 39.41 Gbp, total 2,867.10 Gbp; 66 runs with a base count) · layout PAIRED 66 · platform ILLUMINA 66 · models Illumina NovaSeq X (66) · 0% of runs with a Sandpiper profile · first public 2026-08-06
Downloads
PRJNA1438274.csv.gz (3.1 KB) · parquet (74.1 KB) — all 66 samples, every field with route and confidence · PRJNA1438274_determinations.csv.gz (4.9 KB) — 568 evidence rows