Gut microbiome in critically ill children, case-control
95 faecal samples from children (0-16 years) admitted to a paediatric intensive care unit and healthy controls, studying gut microbiome and bile acid changes during critical illness; case-control design. machine-written summary
95 samples · 95 runs · GB · Child · 2016 · 52.6 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 95 sample values (location site) |
| ✓ Full text | 95 sample values (country) · PMC9213539 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
Schedule stated by the source: “stool at admission and again after 3rd intensive care day; also day1-3,4-7,8-10 bands” (time origin: admission).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 95 | 100% | ||||
| country | 95 | 100% | 95 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| detailed_location | 95 | 100% | ||||
| location_site | 95 | 100% | 95 |
- Profiling gut microbiota and bile acid metabolism in critically ill children. 2022 PMID 35729169 PMC9213539 own_data
Archive description
Critical illness has a damaging effect on normal gut flora and environment. The normal gut microbiota and the products of their metabolism are important in maintaining health locally and systemically. Damage to the gut mucosal lining in severe disease leads to translocation of bacteria or their fragments into the blood stream and may contribute to inflammation, sepsis, multi - organ failure and death. We will examine the effect of critical illness on the gut microbiome - host relationship in children. Children aged 0-16 years admitted to the paediatric intensive care unit (PICU) at Addenbrookes Hospital are eligible for this study alongside healthy controls. We have recruited from three different groups a) Severely ill children with multi - organ failure (failure 2 or more vital organs) b) Less severely ill children (1 organ failure) c) Healthy controls Faecal samples are taken as soon as possible following admission and a subsequent sample as soon as possible after the 3rd intensive care day for metagenomic analysis This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “effect of critical illness on the gut microbiome”
- life stage study.description · “Children aged 0-16 years admitted”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4363646 | country | GB | R3 | 0.70 | paper.fulltext.methods | three paediatric intensive care units (PICUs) in the North Thames Region |
| SAMEA4363646 | location_site | Addenbrooke's Hospital PICU | R4 | 0.45 | ena.study_description | paediatric intensive care unit (PICU) at Addenbrookes Hospital |
Sequencing
95 runs over 95 samples · mean 69.3 Mbp per run (median 52.6 Mbp, total 6.58 Gbp; 95 runs with a base count) · layout PAIRED 95 · platform ILLUMINA 95 · models Illumina MiSeq (95) · 0% of runs with a Sandpiper profile · first public 2016-11-22
Authors (18)
Kean IRL first · Wagner J · Wijeyesekera A · De Goffau M · Thurston S · Clark JA · White DK · Ridout J · Agrawal S · Kayani R · O'Donnell R · Ramnarayan P · Peters MJ · Klein N · Holmes E · Parkhill J · Baker S · Pathan N
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB13830.csv.gz (2.7 KB) · parquet (72.4 KB) — all 95 samples, every field with route and confidence · PRJEB13830_determinations.csv.gz (1.3 KB) — 190 evidence rows