Gut microbiota in ICU C. difficile diarrhea: case-control
14 samples from ICU patients (9 adult, 5 elderly), comparing gut microbiota composition between C. difficile-positive diarrhea, C. difficile-negative diarrhea, and healthy controls; case-control design using 16S rDNA and metagenome sequencing. machine-written summary
14 samples · 14 runs · Adult · 2020 · 5.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 42 sample values (age, collection date, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 56 sample values (location locality, location region, location site, subject id) · PMC7233261 |
| ○ 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 13 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 | 14 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 14 | 100% | 14 | |||
| age_at_collection_days | 14 | 100% | 14 | |||
| collection_date | 14 | 100% | 14 | |||
| detailed_location | 14 | 100% | ||||
| location_locality | 14 | 100% | 14 | |||
| location_region | 14 | 100% | 14 | |||
| location_site | 14 | 100% | 14 | |||
| sex | 14 | 100% | 14 |
- Gut Microbiota Composition Associated With Clostridium difficile-Positive Diarrhea and C. difficile Type in ICU Patients. 2020 PMID 32477962 PMC7233261 own_data
- Functional profile of host microbiome indicates Clostridioides difficile infection. 2022 PMID 36289064 PMC9621045 unsure
Archive description
This study aims to use 16S rDNA (and metagenome) sequencing to compare the microbiota composition of ICU patients with CDpD (CDpD group), ICU patients with C. difficile negative diarrhea (CDnD group), and healthy control subjects (control group), as well as CDpD patients in A+B+, A-B+, and A-B- subgroups.
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 · “Gut microbiota composition associated”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “68 (n=4/14)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN13351573 | age_at_collection_days | 24837.0 | R1 | 0.70 | sample.attr.host_age | 68 |
| SAMN13351573 | collection_date | 2014-06-19 | R1 | 0.90 | biosample.attribute:collection_date | 2014-06-19 |
| SAMN13351573 | location_locality | Changsha | R3 | 0.70 | paper.fulltext.methods | urban tertiary teaching hospital in Changsha, Hunan Province, China |
| SAMN13351573 | location_region | Hunan Province | R3 | 0.70 | paper.fulltext.methods | urban tertiary teaching hospital in Changsha, Hunan Province |
| SAMN13351573 | location_site | Xiangya Hospital | R3 | 0.70 | paper.fulltext.methods | Xiangya Hospital is a 3,500-bed urban tertiary teaching hospital |
| SAMN13351573 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN13351573 | subject_id | SAMN13351573 | R3 | 0.70 | design.one_sample_per_subject:fulltext | 14 samples were selected from these groups (five samples in the CDpD group, four samples in the CDnD group |
Sequencing
14 runs over 14 samples · mean 5.22 Gbp per run (median 5.15 Gbp, total 73.03 Gbp; 14 runs with a base count) · layout PAIRED 14 · platform ILLUMINA 14 · models Illumina HiSeq 2500 (14) · 93% of runs with a Sandpiper profile · first public 2020-05-09
Authors (11)
Duan J first · Meng X · Liu S · Zhou P · Zeng C · Fu C · Dou Q · Wu A · Li C last · Nzabarushimana E first · Tang H last
Downloads
PRJNA591064.csv.gz (1.4 KB) · parquet (70.6 KB) — all 14 samples, every field with route and confidence · PRJNA591064_determinations.csv.gz (1.5 KB) — 98 evidence rows