Healthy gut microbiome in 47 stool samples, Chicago
Cross-sectional study of 47 stool samples from healthy donors in Chicago, IL, used to characterize gut bacterial composition, including respiratory reductase activity in Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae. machine-written summary
47 samples · 47 runs · US · Age unknown · 2022 · 3.21 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 | 389 sample values (age, bmi, collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 47 sample values (location site) |
| ✓ Full text | 94 sample values (health condition, health condition detail) · PMC11055453, PMC11059310, PMC12197998 |
| ○ 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 |
Genera, mean relative abundance over 26 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 | 47 | 100% | ||||
| country | 47 | 100% | 47 | |||
| health_condition | 47 | 100% | 47 | |||
| subject_id | 41 | 87% | 41 | |||
| collection_date | 47 | 100% | 47 | |||
| detailed_location | 47 | 100% | ||||
| health_condition_detail | 47 | 100% | 47 | |||
| latitude | 47 | 100% | 47 | |||
| location_locality | 47 | 100% | 47 | |||
| location_region | 47 | 100% | 47 | |||
| location_site | 47 | 100% | 47 | |||
| longitude | 47 | 100% | 47 | |||
| age_at_collection_days | 22 | 47% | 22 | |||
| bmi | 22 | 47% | 22 | |||
| sex | 22 | 47% | 22 |
- Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease. 2023 PMID 37845315 PMC11059310 own_data
- Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. 2024 PMID 38177297 PMC11055453 own_data
- Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease. 2025 PMID 40574876 PMC12197998 unsure
- The intestinal microbiota impacts nutritional immunity and resistance to <i>Acinetobacter baumannii</i> pneumonia. 2026 PMID 42012958 PMC13123906 unsure
Archive description
DFI at University of Chicago aims to study the bacterial composition of healthy gut and learn about any difference between diseased and healthy individuals.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host study.title · “Healthy Human Stool Donors”
- host run.host_tax_id · “9606”
- body site study.title · “Healthy Human Stool Donors”
- life stage sample.attr.host_age · “24 (n=22/47)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28458695 | age_at_collection_days | 12783.8 | R1 | 0.85 | sample.attr.host_age | 35 |
| SAMN28458695 | bmi | 24.76 | R1 | 0.90 | sample.attr.host_body_mass_index | 24.76479167 |
| SAMN28458695 | collection_date | 2021-08-11 | R1 | 0.90 | biosample.attribute:collection_date | 2021-08-11 |
| SAMN28458695 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Chicago, IL |
| SAMN28458695 | health_condition | healthy_control | R3 | 0.60 | paper.fulltext.results | 262 liver disease patients and 22 healthy donors |
| SAMN28458695 | health_condition_detail | healthy stool donors | R3 | 0.60 | paper.fulltext.results | 262 liver disease patients and 22 healthy donors |
| SAMN28458695 | latitude | 41.8800 | R1 | 0.90 | biosample.attribute:lat_lon | 41.88 N 87.63 W |
| SAMN28458695 | location_locality | Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN28458695 | location_region | Illinois | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN28458695 | location_site | Duchossois Family Institute, University of Chicago | R4 | 0.40 | ena.study_title | Duchossois Family Institute at University of Chicago |
| SAMN28458695 | longitude | -87.6300 | R1 | 0.90 | biosample.attribute:lat_lon | 41.88 N 87.63 W |
| SAMN28458695 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN28458695 | subject_id | DFI0005 | R1 | 0.85 | sample.attr.host_subject_id | DFI0005 |
Sequencing
47 runs over 47 samples · mean 5.33 Gbp per run (median 3.21 Gbp, total 250.60 Gbp; 47 runs with a base count) · layout PAIRED 47 · platform ILLUMINA 47 · models NextSeq 500 (36), Illumina NovaSeq 6000 (11) · 55% of runs with a Sandpiper profile · first public 2022-05-19 – 2026-07-25
Authors (74)
Odenwald MA first · Lin H · Lehmann C · Dylla NP · Cole CG · Mostad JD · Pappas TE · Ramaswamy R · Moran A · Hutchison AL · Stutz MR · Dela Cruz M · Adler E · Boissiere J · Khalid M · Cantoral J · Haro F · Oliveira RA · Waligurski E · Cotter TG · Light SH · Beavis KG · Sundararajan A · Sidebottom AM · Reddy KG · Paul S · Pillai A · Te HS · Rinella ME · Charlton MR · Pamer EG · Aronsohn AI last · Little AS first · Younker IT · Schechter MS · Bernardino PN · Méheust R · Stemczynski J · Scorza K · Mullowney MW · Sharan D · Smith R · Leiter W · Moran D · McMillin M · Iavarone AT · Eren AM · Hernandez A · Rose A · Little J · Sulakhe D · D'Souza M · Woodson C · Tanveer T · de Porto A · Dylla N · Burgo V · Jadczak C · Aronsohn A · Green ER first · Negretti NM · Brunner TH · Shealy NG · Moser FA · Drury SL · Traina KA · Reyes Ruiz VM · Yang TS · Lehmann CJ · Byndloss MX · van de Plas R · Zackular JP · Sucre JMS · Skaar EP last
Downloads
PRJNA838648.csv.gz (2.7 KB) · parquet (74.0 KB) — all 47 samples, every field with route and confidence · PRJNA838648_determinations.csv.gz (5.0 KB) — 530 evidence rows