Pediatric gut microbiota during bowel preparation, China
90 longitudinal stool samples from pediatric colonoscopy patients in Shenzhen, China, collected across five time points around split-dose PEG bowel preparation to study gut microbiota composition and function. machine-written summary
90 samples · 90 runs · CN · Child · 2024 · 10.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 630 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 180 sample values (location locality, location site) |
| ✓ Full text | 270 sample values (antibiotic exposure, health condition, health condition detail) · PMC10390731 |
| ○ 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 |
intervention — arms not resolved
Bowel cleansing / colonoscopy preparation design single_arm_before_after · Split-dose polyethylene glycol (PEG) bowel preparation before colonoscopy
“Split-dose polyethylene glycol (PEG) is routinely used” — abstract:37533931 (study level; per-sample arms are in the intervention column below)
longitudinal
19 of 19 people sampled more than once (90 samples; median 5, up to 5 per person) · follow-up median 32 d (max 36 d) · median interval between samples 10 d (time from collection dates). Schedule stated by the source: “Time_1: 1 day before bowel prep; Check: at colonoscopy; Time_2: 2 days after bowel prep (1 day after colonoscopy); Time_3: 2 weeks after; Time_4: 4 weeks after” (time origin: intervention_start); stated follow-up 28 d.
Each row is one person (19 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 85 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 | 90 | 100% | ||||
| country | 90 | 100% | 90 | |||
| health_condition | 90 | 100% | 90 | |||
| subject_id | 90 | 100% | 90 | |||
| antibiotic_exposure | 90 | 100% | 90 | |||
| collection_date | 90 | 100% | 90 | |||
| detailed_location | 90 | 100% | ||||
| health_condition_detail | 90 | 100% | 90 | |||
| latitude | 90 | 100% | 90 | |||
| location_locality | 90 | 100% | 90 | |||
| location_region | 90 | 100% | 90 | |||
| location_site | 90 | 100% | 90 | |||
| longitude | 90 | 100% | 90 | |||
| timepoint_label | 90 | 100% | 90 |
- Gut microbiota in children with split-dose bowel preparations revealed by metagenomics. 2023 PMID 37533931 PMC10390731 own_data
Archive description
From September to December 2021, a total of 19 pediatric patients undergoing a colonoscopy were enrolled in this study at Shenzhen Children’s Hospital. 90 samples of 19 cases were collected in five time periods and analyzed with metagenomics. Time_1: one day before bowel preparation Time_2: two days after bowel preparation (one day after colonoscopy) Time_3: two weeks after bowel preparation Time_4: four weeks after bowel preparation Check: the bowel fluid from the colonoscopy. They were divided into five groups according to different sampling time, including Time_1, Time_2, Time_3, Time_4 and Check.
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 · “The gut microbiota of children”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “gut microbiota of children with split-dose bowel”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA111378113 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | recently (past 90 days) used probiotics or antibiotics were excluded |
| SAMEA111378113 | collection_date | 2021-07-20 | R1 | 0.90 | biosample.attribute:collection_date | 2021-07-20 |
| SAMEA111378113 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA111378113 | health_condition | other_disease | R3 | 0.70 | paper.fulltext.abstract | pediatric patients undergoing split-dose PEG bowel preparation |
| SAMEA111378113 | health_condition_detail | pediatric patients undergoing a colonoscopy / split-dose PEG bowel preparation | R3 | 0.70 | paper.fulltext.abstract | pediatric patients undergoing split-dose PEG bowel preparation |
| SAMEA111378113 | latitude | 22.5400 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.54 114.08 |
| SAMEA111378113 | location_locality | Shenzhen | R4 | 0.45 | ena.study_description | enrolled in this study at Shenzhen Children’s Hospital |
| SAMEA111378113 | location_region | Guangdong | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.54 114.08 |
| SAMEA111378113 | location_site | Shenzhen Children's Hospital | R4 | 0.45 | ena.study_description | enrolled in this study at Shenzhen Children’s Hospital |
| SAMEA111378113 | longitude | 114.0800 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.54 114.08 |
| SAMEA111378113 | subject_id | 005 | R1 | 0.70 | sample.name_rule:alias | 005-1 |
| SAMEA111378113 | timepoint_label | Time_1 | R1 | 0.70 | sample.name_rule:alias | 005-1 |
Sequencing
90 runs over 90 samples · mean 9.38 Gbp per run (median 10.08 Gbp, total 844.60 Gbp; 90 runs with a base count) · layout PAIRED 90 · platform ILLUMINA 90 · models Illumina NovaSeq 6000 (90) · 94% of runs with a Sandpiper profile · first public 2024-09-19
Downloads
PRJEB56144.csv.gz (3.8 KB) · parquet (75.3 KB) — all 90 samples, every field with route and confidence · PRJEB56144_determinations.csv.gz (8.5 KB) — 1,080 evidence rows