Fecal microbiome and metabolites in MICU patients, Chicago
196 fecal samples from critically ill adults admitted to the MICU in Chicago, IL for non-COVID-19 respiratory failure or shock, studied via shotgun metagenomics and metabolite profiling to assess 30-day mortality risk; case-control design. machine-written summary
196 samples · 196 runs · US · Age unknown · 2024 · 1.81 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 | 1,176 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 784 sample values (health condition, health condition detail, location site, subject id) · PMC12136028, PMC12197998, PMC12788677, PMC13123906 |
| ○ 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: “Fecal specimens collected prospectively during MICU stay; analyses used the first sample after admission, with a subset (65%) collected within 3 days of admission.” (time origin: admission); stated follow-up 30 d.
Genera, mean relative abundance over 176 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 | 196 | 100% | ||||
| country | 196 | 100% | 196 | |||
| health_condition | 196 | 100% | 196 | |||
| subject_id | 196 | 100% | 196 | |||
| collection_date | 196 | 100% | 196 | |||
| detailed_location | 196 | 100% | ||||
| health_condition_detail | 196 | 100% | 196 | |||
| latitude | 196 | 100% | 196 | |||
| location_locality | 196 | 100% | 196 | |||
| location_region | 196 | 100% | 196 | |||
| location_site | 196 | 100% | 196 | |||
| longitude | 196 | 100% | 196 |
- Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality. 2025 PMID 40465720 PMC12136028 own_data
- Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease. 2025 PMID 40574876 PMC12197998 unsure
- Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome. 2026 PMID 41511994 PMC12788677 unsure
- The intestinal microbiota impacts nutritional immunity and resistance to <i>Acinetobacter baumannii</i> pneumonia. 2026 PMID 42012958 PMC13123906 unsure
Archive description
Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments, including stem cell and organ transplantation or following intensive care treatment for COVID-19, and thus might represent a treatable trait to improve clinical outcomes. Whether microbiota derived metabolites are associated with mortality in non-COVID-19 critically ill patients is, however, unknown. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock and correlated microbiota derived metabolites with 30-day mortality. Taxonomic profiling of fecal samples did not correlate with survival outcomes upon correction for confounding variables. Along similar lines, univariate analysis of fecal metabolite concentrations did not identify correlations with mortality in critically ill patients. Multivariable ridge regression analyses using fecal concentrations of 13 microbiota-derived or -modified metabolites, however, enabled development of a metabolic dysbiosis score (MDS) that, independent of potential confounders, predicts survival of critically ill patients with high accuracy, specificity and sensitivity. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “196 critically ill patients”
- body site study.description · “We prospectively collected fecal specimens”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN42394885 | collection_date | 2021-04-07 | R1 | 0.90 | biosample.attribute:collection_date | 2021-04-07 |
| SAMN42394885 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Chicago, IL |
| SAMN42394885 | health_condition | other_disease | R3 | 0.70 | paper.fulltext.abstract | 196 critically ill patients admitted to the MICU |
| SAMN42394885 | health_condition_detail | Critically ill MICU patients with non-COVID-19 respiratory failure or shock | R3 | 0.70 | paper.fulltext.abstract | 196 critically ill patients admitted to the MICU |
| SAMN42394885 | latitude | 41.8800 | R1 | 0.90 | biosample.attribute:lat_lon | 41.88 N 87.63 W |
| SAMN42394885 | location_locality | Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN42394885 | location_region | Illinois | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN42394885 | location_site | University of Chicago Medical Center | R3 | 0.70 | paper.fulltext.methods | performed at the University of Chicago Medical Center |
| SAMN42394885 | longitude | -87.6300 | R1 | 0.90 | biosample.attribute:lat_lon | 41.88 N 87.63 W |
| SAMN42394885 | subject_id | SAMN42394885 | R3 | 0.70 | design.one_sample_per_subject:fulltext | One hundred ninety-six MICU patients without COVID-19 produced a fecal sample that was analyzable for metagenomics and metabolomics |
Sequencing
196 runs over 196 samples · mean 2.05 Gbp per run (median 1.81 Gbp, total 401.27 Gbp; 196 runs with a base count) · layout PAIRED 196 · platform ILLUMINA 196 · models Illumina NovaSeq 6000 (196) · 90% of runs with a Sandpiper profile · first public 2024-07-11
Authors (59)
de Porto AP first · Dylla NP · Stutz M · Lin H · Khalid M · Mullowney MW · Little J · Rose A · Moran D · McMillin M · Burgo V · Smith R · Woodson C · Metcalfe C · Ramaswamy R · Lehmann C · Odenwald M · Bandealy N · Zhao J · Kim M · Adler E · Sundararajan A · Sidebottom A · Kress JP · Wolfe KS · Pamer EG · Patel BK last · Odenwald MA first · Moran A · Sidebottom AM · Hernandez A · Sulakhe D · D'Souza M · Tanveer T · de Porto A · Dylla N · Cantoral J · Jadczak C · Aronsohn A · Rinella ME last · Rose AR · Nguyen AB · Lehmann CJ · Yeo KJ · Green ER first · Negretti NM · Brunner TH · Shealy NG · Moser FA · Drury SL · Traina KA · Reyes Ruiz VM · Yang TS · Byndloss MX · van de Plas R · Zackular JP · Light SH · Sucre JMS · Skaar EP last
Downloads
PRJNA1134172.csv.gz (6.6 KB) · parquet (80.6 KB) — all 196 samples, every field with route and confidence · PRJNA1134172_determinations.csv.gz (13.1 KB) — 1,960 evidence rows