Gut Microbiome in COVID-19 ICU Patients, Chicago
Fecal samples from 71 critically ill COVID-19 patients admitted to a Chicago, IL medical ICU were analyzed by shotgun metagenomics in a longitudinal study linking gut microbiome and metabolite composition to respiratory failure and mortality outcomes. machine-written summary
71 samples · 71 runs · US · Age unknown · 2022 · 1.68 Gbp / sample · cohort Fecal Butyrate and Deoxycholic Acid Concentrations
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 778 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 71 sample values (subject id) · PMC9633022 |
| ○ 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 |
age: two sequence archives disagree for 1 sample (e.g. 58.0 vs 21180.5) — withheld.
The sources disagree on 1 sample. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN28789124 | age | 58.0 (sequence archive) | 21180.5 (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 64 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 | 71 | 100% | ||||
| country | 71 | 100% | 71 | |||
| health_condition | 71 | 100% | 71 | |||
| subject_id | 71 | 100% | 71 | |||
| bmi | 71 | 100% | 71 | |||
| collection_date | 71 | 100% | 71 | |||
| detailed_location | 71 | 100% | ||||
| health_condition_detail | 71 | 100% | 71 | |||
| latitude | 71 | 100% | 71 | |||
| location_locality | 71 | 100% | 71 | |||
| location_region | 71 | 100% | 71 | |||
| longitude | 71 | 100% | 71 | |||
| age_at_collection_days | 70 | 99% | 70 | |||
| sex | 69 | 97% | 69 |
- Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure. 2022 PMID 36329015 PMC9633022 own_data
- Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease. 2025 PMID 40574876 PMC12197998 unsure
Archive description
This study is designed to study the variations in the microbiome among critically ill patients and the effect of admission to the medical intensive care unit (MICU) at the University of Chicago. Additionally, we will examine the downstream clinical effects of dysbiosis in ICU patients and how patients maybe effected long term. By longitudinally sampling patients throughout their MICU admission and correlating changes in the microbiome with clinical data, this study will identify factors that impact the composition of the microbiome and their impact on clinical outcomes. These associations will be the foundation for further clinical studies and clinical trials to optimize the human microbiome in patients in the critical care unit.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host study.description · “microbiome among critically ill patients”
- body site sample.attr.isolation_source · “human stool (n=71/71)”
- life stage sample.attr.host_age · “63.32876712 (n=36/71)”
- life stage sample.attr.host_age · “29.20821918 (n=33/71)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28789121 | age_at_collection_days | 34394.0 | R1 | 0.85 | sample.attr.host_age | 94.06575342 |
| SAMN28789121 | bmi | 22.39 | R1 | 0.90 | sample.attr.host_body_mass_index | 22.39 |
| SAMN28789121 | collection_date | 2021-02-04 | R1 | 0.90 | biosample.attribute:collection_date | 2021-02-04 |
| SAMN28789121 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Chicago, IL |
| SAMN28789121 | health_condition | other_infection | R1 | 0.85 | biosample_attr | SARS-CoV-2 |
| SAMN28789121 | health_condition_detail | SARS-CoV-2 | R1 | 0.90 | sample.attr.host_disease | SARS-CoV-2 |
| SAMN28789121 | latitude | 41.7900 | R1 | 0.90 | biosample.attribute:lat_lon | 41.79 N 87.60 W |
| SAMN28789121 | location_locality | Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN28789121 | location_region | Illinois | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN28789121 | longitude | -87.6000 | R1 | 0.90 | biosample.attribute:lat_lon | 41.79 N 87.60 W |
| SAMN28789121 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN28789121 | subject_id | SAMN28789121 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Of these, 71 patients produced a fecal sample within 72 h of enrollment |
Sequencing
71 runs over 71 samples · mean 1.83 Gbp per run (median 1.68 Gbp, total 129.97 Gbp; 71 runs with a base count) · layout PAIRED 71 · platform ILLUMINA 71 · models Illumina NovaSeq 6000 (71) · 90% of runs with a Sandpiper profile · first public 2022-06-21
Authors (44)
Stutz MR first · Dylla NP · Pearson SD · Lecompte-Osorio P · Nayak R · Khalid M · Adler E · Boissiere J · Lin H · Leiter W · Little J · Rose A · Moran D · Mullowney MW · Wolfe KS · Lehmann C · Odenwald M · De La Cruz M · Giurcanu M · Pohlman AS · Hall JB · Chaubard JL · Sundararajan A · Sidebottom A · Kress JP · Pamer EG · Patel BK last · Odenwald MA first · Ramaswamy R · Moran A · Sidebottom AM · Hernandez A · McMillin M · Sulakhe D · D'Souza M · Woodson C · Tanveer T · de Porto A · Dylla N · Burgo V · Cantoral J · Jadczak C · Aronsohn A · Rinella ME last
Downloads
PRJNA842425.csv.gz (3.8 KB) · parquet (75.7 KB) — all 71 samples, every field with route and confidence · PRJNA842425_determinations.csv.gz (7.9 KB) — 849 evidence rows