Gut microbiota in critically ill children, Shanghai, case-control
142 anal swab samples from children in Shanghai, China, comparing gut microbiota between sepsis patients and healthy controls in a case-control study examining PICU treatment effects on microbial diversity and antimicrobial resistance genes. machine-written summary
142 samples · 142 runs · CN · Child · 2023 · 0.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,097 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 142 sample values (location site) |
| ✓ Full text | 426 sample values (antibiotic exposure, health condition, health condition detail) · PMC10679412, PMC12834510 |
| ○ 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
71 of 71 people sampled more than once (142 samples; median 2, up to 2 per person) · follow-up median 7 d (max 48 d) · median interval between samples 7 d (time from collection dates). Schedule stated by the source: “Anal swabs collected on days 1 (D1) and 7 (D7) of PICU admission” (time origin: admission); stated follow-up 28 d.
Each row is one person (36 shown of 71); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 80 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 | 142 | 100% | ||||
| country | 142 | 100% | 142 | |||
| health_condition | 142 | 100% | 142 | |||
| subject_id | 142 | 100% | 142 | |||
| antibiotic_exposure | 142 | 100% | 142 | |||
| collection_date | 142 | 100% | 142 | |||
| detailed_location | 142 | 100% | ||||
| health_condition_detail | 142 | 100% | 142 | |||
| latitude | 142 | 100% | 142 | |||
| location_locality | 142 | 100% | 142 | |||
| location_site | 142 | 100% | 142 | |||
| longitude | 142 | 100% | 142 | |||
| timepoint_label | 142 | 100% | 142 | |||
| location_region | 103 | 73% | 103 |
- Pediatric intensive care unit treatment alters the diversity and composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children. 2023 PMID 38029168 PMC10679412 own_data
- Dysbiosis and metabolic pathway shifts in the gut microbiome of children with sepsis: a comparative analysis. 2025 PMID 41602763 PMC12834510 own_data
Archive description
This study aimed to investigate the changes in the characteristics of the gut microbiota in critically ill children after short-term pediatric intensive care unit (PICU) treatments
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “Composition of the Gut Microbiota and Antimicrobial”
- body site study.description · “characteristics of the gut microbiota in critically”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “Pediatric Intensive Care Unit”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38034349 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.methods | receiving broad-spectrum antibiotics within the first 24 h |
| SAMN38034349 | collection_date | 2021-09-19 | R1 | 0.90 | biosample.attribute:collection_date | 2021-09-19 |
| SAMN38034349 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:shanghai |
| SAMN38034349 | health_condition | other_disease | R3 | 0.70 | paper.fulltext.methods | prospective observational study on children admitted to the PICU |
| SAMN38034349 | health_condition_detail | critically ill children admitted to PICU receiving broad-spectrum antibiotic therapy | R3 | 0.70 | paper.fulltext.methods | prospective observational study on children admitted to the PICU |
| SAMN38034349 | latitude | 31.2700 | R1 | 0.90 | biosample.attribute:lat_lon | 31.27 N 121.52 E |
| SAMN38034349 | location_locality | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China:shanghai |
| SAMN38034349 | location_region | Shanghai Shi | R1 | 0.60 | biosample.attribute:lat_lon | 31.27 N 121.52 E |
| SAMN38034349 | location_site | Xinhua Hospital | R4 | 0.50 | paper.abstract | admitted to the PICU of Xinhua Hospital |
| SAMN38034349 | longitude | 121.5200 | R1 | 0.90 | biosample.attribute:lat_lon | 31.27 N 121.52 E |
| SAMN38034349 | subject_id | S1 | R1 | 0.70 | sample.name_rule:title | S1 |
| SAMN38034349 | timepoint_label | D1 | R1 | 0.70 | sample.name_rule:title+collection_date | S1 |
Sequencing
142 runs over 142 samples · mean 0.43 Gbp per run (median 0.15 Gbp, total 61.14 Gbp; 142 runs with a base count) · layout SINGLE 142 · platform ILLUMINA 142 · models Illumina NovaSeq 6000 (142) · 57% of runs with a Sandpiper profile · first public 2023-11-01
Downloads
PRJNA1033539.csv.gz (5.5 KB) · parquet (78.6 KB) — all 142 samples, every field with route and confidence · PRJNA1033539_determinations.csv.gz (15.0 KB) — 1,665 evidence rows