Gut dysbiosis in cancer, IBD, and C. difficile, Warsaw
244 fecal samples from hospitalized cancer patients, IBD patients, and healthy controls in Warsaw, Poland, comparing gut microbiota and metabolite profiles with and without C. difficile infection in a case-control design. machine-written summary
244 samples · 244 runs · PL · Age unknown · 2023 · 4.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,745 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude, subject id) |
| ✓ Abstract / description | 45 sample values (health condition detail) |
| ✓ Full text | 54 sample values (collection date) · PMC10413277 |
| ○ 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 |
longitudinal
12 of 165 people sampled more than once (28 samples; median 2, up to 4 per person) · follow-up median 18 d (max 12 mo) · median interval between samples 9 d (time from collection dates).
Each row is one person (10 shown of 12); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 225 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 | 244 | 100% | 244 | |||
| health_condition | 199 | 82% | 199 | |||
| subject_id | 181 | 74% | 181 | |||
| collection_date | 244 | 100% | 190 | 54 | ||
| detailed_location | 244 | 100% | ||||
| health_condition_detail | 244 | 100% | 199 | 45 | ||
| latitude | 244 | 100% | 244 | |||
| location_locality | 244 | 100% | 244 | |||
| longitude | 244 | 100% | 244 |
- Diarrheal-associated gut dysbiosis in cancer and inflammatory bowel disease patients is exacerbated by Clostridioides difficile infection. 2023 PMID 37577378 PMC10413277 own_data
Archive description
In this study, we used shotgun metagenomic sequencing and GC/MS metabolomics to compare the microbiota profiles and metabolite levels of hospitalized cancer patients with healthcare-associated diarrhea, patients with IBD, and healthy controls. Our data define a role of CDI in modulating low diversity dysbiosis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “diarrhoeal-associated gut dysbiosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33941250 | collection_date | 2021-01-14 | R1 | 0.90 | biosample.attribute:collection_date | 2021-01-14 |
| SAMN33941285 | collection_date | 2021-01/2021-06 | R3 | 0.70 | paper.fulltext.methods | Between January and June 2021, a total of 226 participants |
| SAMN33941250 | country | PL | R1 | 0.90 | sample.attr.geo_loc_name | Poland:Warsaw |
| SAMN33941250 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | cancer - gastrointestinal |
| SAMN33941250 | health_condition_detail | cancer | R1 | 0.90 | sample.attr.gastrointest_disord | cancer |
| SAMN34081129 | health_condition_detail | mixed_case_control: cancer patients with diarrhea vs IBD patients vs healthy controls | R4 | 0.50 | study.description | cancer patients with healthcare-associated diarrhea, patients with IBD, and healthy controls |
| SAMN33941250 | latitude | 52.1400 | R1 | 0.90 | biosample.attribute:lat_lon | 52.14 N 21 E |
| SAMN33941250 | location_locality | Warszawa | R1 | 0.75 | biosample.attribute:geo_loc_name | Poland:Warsaw |
| SAMN33941250 | longitude | 21.0000 | R1 | 0.90 | biosample.attribute:lat_lon | 52.14 N 21 E |
| SAMN33941250 | subject_id | 7874 | R1 | 0.85 | sample.attr.host_subject_id | 7874 |
Sequencing
244 runs over 244 samples · mean 4.36 Gbp per run (median 4.20 Gbp, total 1,064.67 Gbp; 244 runs with a base count) · layout PAIRED 244 · platform ILLUMINA 244 · models Illumina NovaSeq 6000 (244) · 93% of runs with a Sandpiper profile · first public 2023-07-13
Authors (12)
Kulecka M first · Zeber-Lubecka N · Bałabas A · Czarnowski P · Bagińska K · Głowienka M · Kluska A · Piątkowska M · Dąbrowska M · Waker E · Mikula M · Ostrowski J last
Downloads
PRJNA943135.csv.gz (7.9 KB) · parquet (81.3 KB) — all 244 samples, every field with route and confidence · PRJNA943135_determinations.csv.gz (13.4 KB) — 1,844 evidence rows