Multi-omics of C. difficile infection diarrheal stool, USA
75 diarrheal stool samples from Pennsylvania, USA, comparing C. difficile infection-positive and -negative patients using matched 16S, ITS, metagenomic and metatranscriptomic sequencing in a case-control design. machine-written summary
75 samples · 75 runs · US · Age unknown · 2018 · 68.6 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 450 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 49 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC6714892 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 52 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
26 of 49 people sampled more than once (52 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 18 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 | 75 | 100% | 75 | |||
| health_condition | 26 | 35% | 26 | |||
| subject_id | 75 | 100% | 75 | |||
| collection_date | 75 | 100% | 75 | |||
| detailed_location | 75 | 100% | ||||
| health_condition_detail | 75 | 100% | 26 | 49 | ||
| latitude | 75 | 100% | 75 | |||
| location_region | 75 | 100% | 75 | |||
| longitude | 75 | 100% | 75 |
- Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection. 2019 PMID 31462412 PMC6714892 own_data
Archive description
Here, we provide matched 16S,ITS,Metagenome and Metatranscriptome data obtained from CDI- and CDI+ diarrheal samples.
How this project entered the registry
Classified as human gut / stool mixed assays of age unknown by opus_adjudicated with confidence 0.40. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “CDI- and CDI+ diarrheal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09534375 | collection_date | 2017-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01-01 |
| SAMN09534375 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Pennsylvania |
| SAMN09534375 | health_condition | gi_infection_or_diarrhoea | R2 | 0.75 | external.gmrepo source | phenotype: Clostridium Infections |
| SAMN09534375 | health_condition_detail | Clostridium Infections | R2 | 0.75 | external.gmrepo source | phenotype: Clostridium Infections |
| SAMN09534428 | health_condition_detail | mixed_case_control: 18 CDI-positive inpatients, 31 CDI-negative inpatients; mixed case-control design | R4 | 0.50 | paper.abstract | CDI-positive and -negative patients |
| SAMN09534375 | latitude | 40.2647 | R1 | 0.90 | biosample.attribute:lat_lon | 40.2647 N 76.6763 W |
| SAMN09534375 | location_region | Pennsylvania | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Pennsylvania |
| SAMN09534375 | longitude | -76.6763 | R1 | 0.90 | biosample.attribute:lat_lon | 40.2647 N 76.6763 W |
| SAMN09534375 | subject_id | 13 | R1 | 0.70 | sample.name_rule:alias | 13MG |
Sequencing
75 runs over 75 samples · mean 0.78 Gbp per run (median 68.6 Mbp, total 58.71 Gbp; 75 runs with a base count) · layout PAIRED 75 · platform ILLUMINA 75 · models Illumina MiSeq (49), Illumina HiSeq 4000 (26) · 24% of runs with a Sandpiper profile · first public 2018-07-03
Authors (11)
Stewart DB first · Wright JR · Fowler M · McLimans CJ · Tokarev V · Amaniera I · Baker O · Wong HT · Brabec J · Drucker R · Lamendella R last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA478949.csv.gz (2.8 KB) · parquet (73.5 KB) — all 75 samples, every field with route and confidence · PRJNA478949_determinations.csv.gz (5.2 KB) — 551 evidence rows