Hi-C gut metagenomics, chronically critically ill, Moscow
4 longitudinal stool samples from chronically critically ill ICU patients with severe brain injury in Moscow, Russia, analyzed using shotgun metagenomics and Hi-C to study gut microbiome dynamics. machine-written summary
4 samples · 4 runs · RU · Adult · 2021 · 35.95 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 40 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8851603 |
| ○ 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 — not resolved
Schedule stated by the source: “Stool collected at 2 time points per patient (n=2 patients), 1-2 week interval; 2nd sample day 7 (patient A) or day 14 (patient B)”; stated follow-up 14 d.
Genera, mean relative abundance over 1 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 | 4 | 100% | ||||
| country | 4 | 100% | 4 | |||
| health_condition | 4 | 100% | 4 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 4 | 100% | 4 | |||
| collection_date | 4 | 100% | 4 | |||
| detailed_location | 4 | 100% | ||||
| health_condition_detail | 4 | 100% | 4 | |||
| latitude | 4 | 100% | 4 | |||
| location_locality | 4 | 100% | 4 | |||
| location_region | 4 | 100% | 4 | |||
| longitude | 4 | 100% | 4 | |||
| sex | 4 | 100% | 4 |
- Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients. 2021 PMID 35185811 PMC8851603 own_data
Archive description
A pilot study to evaluate the dynamics of gut microbial community structure and functions in Intensive care unit patients using a combination of high-throughput "shotgun" metagenomics and chromosome conformation capture (Hi-C).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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 · “Hi-C metagenomics of gut microbiome in chronically”
- body site study.description · “the dynamics of gut microbial community structure”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “74 (n=4/4)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18524910 | age_at_collection_days | 27394.0 | R1 | 0.85 | sample.attr.host_age | 75 |
| SAMN18524910 | collection_date | 2020-04-15 | R1 | 0.90 | biosample.attribute:collection_date | 2020-04-15 |
| SAMN18524910 | country | RU | R1 | 0.90 | sample.attr.geo_loc_name | Russia:Moscow |
| SAMN18524910 | health_condition | cardiometabolic_other | R1 | 0.90 | biosample_attr | intracerebral hemorrhage |
| SAMN18524910 | health_condition_detail | intracerebral hemorrhage | R1 | 0.90 | sample.attr.host_disease | intracerebral hemorrhage |
| SAMN18524910 | latitude | 56.0200 | R1 | 0.90 | biosample.attribute:lat_lon | 56.020 N 36.987 E |
| SAMN18524910 | location_locality | Moscow | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia:Moscow |
| SAMN18524910 | location_region | Moscow | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia:Moscow |
| SAMN18524910 | longitude | 36.9870 | R1 | 0.90 | biosample.attribute:lat_lon | 56.020 N 36.987 E |
| SAMN18524910 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
Sequencing
4 runs over 4 samples · mean 36.04 Gbp per run (median 35.95 Gbp, total 144.18 Gbp; 4 runs with a base count) · layout PAIRED 4 · platform ILLUMINA 4 · models Illumina HiSeq 2500 (4) · 25% of runs with a Sandpiper profile · first public 2021-08-25
Authors (12)
Ivanova V first · Chernevskaya E · Vasiluev P · Ivanov A · Tolstoganov I · Shafranskaya D · Ulyantsev V · Korobeynikov A · Razin SV · Beloborodova N · Ulianov SV · Tyakht A last
Downloads
PRJNA718195.csv.gz (1.0 KB) · parquet (70.5 KB) — all 4 samples, every field with route and confidence · PRJNA718195_determinations.csv.gz (965 B) — 40 evidence rows