Gut microbiomes of healthy adults from St. Louis
289 fecal samples from 20 healthy adult volunteers in St. Louis, collected over 6 months in a longitudinal study. machine-written summary
289 samples · 289 runs · US · Adult · 2022 · 1.18 Gbp / sample · cohort Commensal-pathogen dynamics structure disease outc
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,870 sample values (antibiotic exposure, collection date, country, latitude, location locality, location region, longitude, sex) |
| ✓ Abstract / description | 538 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10536327, PMC11133793, PMC11717617, PMC9066705 |
| ✓ Supplementary tables | 60 sample values (health condition, health condition detail, subject id) |
| – 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population healthy_control · 4 common antibiotic regimens, pre/post sampling 6 months
“exposure to 4 commonly used antibiotic regimens” — abstract:35417701 (study level; per-sample arms are in the intervention column below)
longitudinal
20 of 40 people sampled more than once (269 samples; median 14, up to 14 per person) · follow-up median 6 mo (max 18 mo) · median interval between samples 5 d (time from collection dates). Schedule stated by the source: “6 month longitudinal study, fecal metagenomes collected”.
Each row is one person (20 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 263 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 | 289 | 100% | ||||
| country | 289 | 100% | 289 | |||
| health_condition | 289 | 100% | 20 | 269 | ||
| subject_id | 289 | 100% | 269 | 20 | ||
| antibiotic_exposure | 289 | 100% | 289 | |||
| collection_date | 289 | 100% | 289 | |||
| detailed_location | 289 | 100% | ||||
| health_condition_detail | 289 | 100% | 20 | 269 | ||
| latitude | 289 | 100% | 289 | |||
| location_locality | 289 | 100% | 289 | |||
| location_region | 289 | 100% | 289 | |||
| longitude | 289 | 100% | 289 | |||
| sex | 289 | 100% | 289 | |||
| timepoint_label | 289 | 100% | 289 |
- Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. 2022 PMID 35417701 PMC9066705 unsure
- Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance. 2023 PMID 37764709 PMC10536327 unsure
- Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study. 2024 PMID 38813445 PMC11133793 unsure
- Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. 2025 PMID 39731916 PMC11717617 unsure
Archive description
6 month Longitudinal study of fecal metagenomes collected from a 20 volunteer cohort from the St. Louis area.
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 · “Fecal metagenomes of healthy”
- body site study.description · “Longitudinal study of fecal metagenomes collected from”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.title · “metagenomes of healthy volunteers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18812905 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:chem_administration | Azithromycin |
| SAMN18812905 | collection_date | 2017-01-09 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01-09 |
| SAMN18812905 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: St. Louis |
| SAMN18812905 | health_condition | healthy_control | R2 | 0.85 | paper.supp.mmc5.xlsx[Accession_group_study!group] | Accession =SRS8744671; group=Control |
| SAMN18812906 | health_condition | healthy_control | R4 | 0.50 | study.title | healthy volunteers |
| SAMN18812905 | health_condition_detail | Control | R2 | 0.85 | paper.supp.mmc5.xlsx[Accession_group_study!group] | Accession =SRS8744671; group=Control |
| SAMN18812906 | health_condition_detail | healthy volunteers | R4 | 0.50 | study.title | healthy volunteers |
| SAMN18812905 | latitude | 38.6270 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN18812905 | location_locality | St. Louis | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: St. Louis |
| SAMN18812905 | location_region | Missouri | R1 | 0.60 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN18812905 | longitude | -90.1994 | R1 | 0.90 | biosample.attribute:lat_lon | 38.6270 N 90.1994 W |
| SAMN18812905 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN18812906 | subject_id | 01 | R1 | 0.70 | sample.name_rule:sample_alias | 01_S02 |
| SAMN18812905 | subject_id | HH-1 | R2 | 0.85 | paper.supp.mmc5.xlsx[Accession_group_study!Patient_ID] | Accession =SRS8744671; Patient_ID=HH-1 |
| SAMN18812905 | timepoint_label | 01 | R1 | 0.70 | sample.name_rule:sample_alias | 01_S01 |
Sequencing
289 runs over 289 samples · mean 1.31 Gbp per run (median 1.18 Gbp, total 378.81 Gbp; 289 runs with a base count) · layout PAIRED 289 · platform ILLUMINA 289 · models NextSeq 500 (289) · 91% of runs with a Sandpiper profile · first public 2022-04-13
Authors (52)
Anthony WE first · Wang B · Sukhum KV · D'Souza AW · Hink T · Cass C · Seiler S · Reske KA · Coon C · Dubberke ER · Burnham CD · Dantas G · Kwon JH last · Chen J first · Zhu J · Lu W · Wang H · Pan M · Tian P · Zhao J · Zhang H · Chen W last · Choi J first · Thänert R · Nickel KB · Olsen MA · Thänert A · Wallace MA · Barlet MH · Struttmann EL · Iqbal ZH · Sax SR · Fraser VJ · Baker AW · Foy KR · Williams B · Xu B · Capocci-Tolomeo P · Lautenbach E · CDC Prevention Epicenters Program last · Fishbein SRS first · DeVeaux AL · Khanna S · Ferreiro AL · Liao J · Agee W · Ning J · Mahmud B · Wallace MJ · Guruge J · Leekha S · Rengarajan S
Downloads
PRJNA664754.csv.gz (8.8 KB) · parquet (82.0 KB) — all 289 samples, every field with route and confidence · PRJNA664754_determinations.csv.gz (28.5 KB) — 3,468 evidence rows