Gut microbiota decline in ICU patients, Birmingham UK
233 longitudinal faecal samples from adult ICU patients in Birmingham, UK, studied by shotgun metagenomics to track loss of gut microbial diversity and pathogen domination during critical illness. machine-written summary
233 samples · 233 runs · GB · Age unknown · 2019 · 1.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,398 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 699 sample values (health condition, health condition detail, location site) · PMC6807385 |
| ✓ Supplementary tables | 231 sample values (subject id) |
| – 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
design observational_with_procedure
longitudinal — not resolved
24 of 24 people sampled more than once (231 samples; median 8, up to 22 per person). Schedule stated by the source: “Serial daily faecal samples per patient during ICU stay; no fixed numeric day offsets stated” (time origin: ICU admission).
Genera, mean relative abundance over 133 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 | 233 | 100% | ||||
| country | 233 | 100% | 233 | |||
| health_condition | 233 | 100% | 233 | |||
| subject_id | 231 | 99% | 231 | |||
| collection_date | 233 | 100% | 233 | |||
| detailed_location | 233 | 100% | ||||
| health_condition_detail | 233 | 100% | 233 | |||
| latitude | 233 | 100% | 233 | |||
| location_locality | 233 | 100% | 233 | |||
| location_region | 233 | 100% | 233 | |||
| location_site | 233 | 100% | 233 | |||
| longitude | 233 | 100% | 233 |
- Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients. 2019 PMID 31526447 PMC6807385 own_data
Archive description
The microbial community in Intensive Care Unit patients plays a key role in determining the balance between health and disease. Here, we describe a prospective observational study of 25 ICU patients in which serial faecal samples were subjected to shotgun metagenome sequencing, phylogenetic profiling and microbial genome analyses.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “25 ICU patients”
- body site study.description · “serial faecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11258315 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN11258315 | country | GB | R1 | 0.90 | sample.attr.geo_loc_name | United Kingdom: Birmingham |
| SAMN11258315 | health_condition | other_disease | R3 | 0.70 | paper.fulltext.abstract | prospective observational study of 24 ICU patients |
| SAMN11258315 | health_condition_detail | critically ill ICU patients | R3 | 0.70 | paper.fulltext.abstract | prospective observational study of 24 ICU patients |
| SAMN11258315 | latitude | 52.4900 | R1 | 0.90 | biosample.attribute:lat_lon | 52.49 N 1.89 W |
| SAMN11258315 | location_locality | Birmingham | R1 | 0.85 | biosample.attribute:geo_loc_name | United Kingdom: Birmingham |
| SAMN11258315 | location_region | England | R1 | 0.60 | biosample.attribute:lat_lon | 52.49 N 1.89 W |
| SAMN11258315 | location_site | Queen Elizabeth Hospital Birmingham, Intensive Care Unit | R3 | 0.70 | paper.fulltext.methods | Queen Elizabeth Hospital Birmingham is a university teaching hospital |
| SAMN11258315 | longitude | -1.8900 | R1 | 0.90 | biosample.attribute:lat_lon | 52.49 N 1.89 W |
| SAMN11258315 | subject_id | Patient 2 | R2 | 0.85 | paper.supp.mgen-5-293-s002.xlsx[Table S1!Patient] | Patient 2 |
Sequencing
233 runs over 233 samples · mean 2.09 Gbp per run (median 1.51 Gbp, total 487.52 Gbp; 233 runs with a base count) · layout PAIRED 233 · platform ILLUMINA 233 · models NextSeq 550 (233) · 57% of runs with a Sandpiper profile · first public 2019-04-20
Authors (13)
Ravi A first · Halstead FD · Bamford A · Casey A · Thomson NM · van Schaik W · Snelson C · Goulden R · Foster-Nyarko E · Savva GM · Whitehouse T · Pallen MJ · Oppenheim BA last
Downloads
PRJNA533528.csv.gz (6.1 KB) · parquet (78.7 KB) — all 233 samples, every field with route and confidence · PRJNA533528_determinations.csv.gz (13.5 KB) — 2,328 evidence rows