Longitudinal gut metagenomes from UK ICU patients
60 longitudinal stool samples from adult ICU patients in the United Kingdom, sequenced by Illumina metagenomics and Nanopore viromics (human reads removed; Lactococcus phage Q33 spiked into VLP libraries as a control). machine-written summary
60 samples · 83 runs · GB · Adult · 2023 · 6.02 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 393 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 120 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
5 of 5 people sampled more than once (57 samples; median 12, up to 18 per person) · follow-up median 17 d (max 37 d) · median interval between samples 2 d (time from collection dates). Schedule stated by the source: “stool samples at multiple timepoints per patient, e.g. days 1,2,3,5,7,9,10,12”.
Each row is one person (5 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 44 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 | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 60 | 100% | 60 | |||
| subject_id | 57 | 95% | 57 | |||
| collection_date | 60 | 100% | 60 | |||
| health_condition_detail | 60 | 100% | 60 | |||
| detailed_location | 57 | 95% | ||||
| latitude | 57 | 95% | 57 | |||
| location_region | 57 | 95% | 57 | |||
| longitude | 57 | 95% | 57 | |||
| timepoint_label | 45 | 75% | 45 |
Archive description
Illumina metagenomic sequencing of longitudinal stool samples from five ICU patients. Nanopore sequencing of virus-like-particles extracted from the same stool samples. Human reads have been removed from both Illumina and Nanopore reads. Lactococcus phage Q33 was spiked into the Nanopore VLP libraries.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult 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 · “of ICU patient stool samples”
- body site study.description · “sequencing of longitudinal stool samples from five”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114405826 | collection_date | 2021-08-28 | R1 | 0.90 | biosample.attribute:collection_date | 2021-08-28 |
| SAMEA114405826 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA114405826 | health_condition | other_disease | R4 | 0.40 | study.title | ICU patient stool samples |
| SAMEA114405826 | health_condition_detail | ICU patients (critical illness, unspecified) | R4 | 0.40 | study.title | ICU patient stool samples |
| SAMEA114405826 | latitude | 52.4510 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.45101153 -1.93917291 |
| SAMEA114405826 | location_region | England | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.45101153 -1.93917291 |
| SAMEA114405826 | longitude | -1.9392 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.45101153 -1.93917291 |
| SAMEA114405826 | subject_id | A | R1 | 0.70 | sample.name_rule:sample_alias | A1 |
| SAMEA114405826 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:sample_alias | A1 |
Sequencing
83 runs over 60 samples · mean 3.96 Gbp per run (median 5.34 Gbp, total 328.77 Gbp; 83 runs with a base count) · layout PAIRED 48, SINGLE 35 · platform ILLUMINA 48, OXFORD_NANOPORE 35 · models Illumina NovaSeq 6000 (48), MinION (35) · 53% of runs with a Sandpiper profile · first public 2023-09-21 – 2023-09-25
Authors (0)
No author record.
Downloads
PRJEB66265.csv.gz (2.7 KB) · parquet (72.6 KB) — all 60 samples, every field with route and confidence · PRJEB66265_determinations.csv.gz (4.4 KB) — 513 evidence rows