Gut E. coli in recurrent UTI case-control study, St. Louis
422 stool samples from women in St. Louis, MO, USA, comparing gut E. coli (via E. coli PanSelect enrichment) between recurrent UTI cases and healthy controls, in a case-control design. machine-written summary
422 samples · 721 runs · US · Age unknown · 2017 · 3.76 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,160 sample values (collection date, country, location locality, location region, subject id, timepoint) |
| ✓ Abstract / description | 232 sample values (health condition detail) |
| ✓ Full text | 422 sample values (sex) · PMC11133793, PMC11530686, PMC12122369, PMC8900328, PMC9136705 |
| ✓ Supplementary tables | 292 sample values (health condition, health condition detail, timepoint) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
31 of 31 people sampled more than once (422 samples; median 13, up to 24 per person) · follow-up median 23 d (max 12 mo) · median interval between samples 36 d (time from collection dates). Schedule stated by the source: “year-long longitudinal stool sampling of women with recurrent UTI, numbered timepoints per subject (e.g. UMB05_04, UMB05_05, UMB05_06)” (time origin: enrolment); stated follow-up 12 mo.
Each row is one person (3 shown of 31); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 387 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 | 0 | 0% | ||||
| country | 422 | 100% | 422 | |||
| health_condition | 97 | 23% | 97 | |||
| subject_id | 422 | 100% | 422 | |||
| detailed_location | 422 | 100% | ||||
| health_condition_detail | 422 | 100% | 190 | 232 | ||
| location_locality | 422 | 100% | 422 | |||
| location_region | 422 | 100% | 422 | |||
| sex | 422 | 100% | 422 | |||
| collection_date | 298 | 71% | 298 | |||
| timepoint_label | 179 | 42% | 174 | 5 |
- StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities. 2022 PMID 35255937 PMC8900328 own_data
- Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women. 2022 PMID 35505248 PMC9136705 own_data
- Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. 2024 PMID 39487120 PMC11530686 own_data
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain. 2025 PMID 40328944 PMC12122369 own_data
- Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study. 2024 PMID 38813445 PMC11133793 unsure
Archive description
Metagenomic samples extracted from Stool of UI cases/control patients and 16S sequenced
How this project entered the registry
Classified as human gut / stool / vaginal / urogenital shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.53. Assay shotgun_dna.
- host study.description · “Stool of UI cases/control patients”
- body site study.description · “Stool of UI cases/control patients”
- body site sample.attr.isolation_source · “urine (n=93/515)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07583764 | collection_date | 2015-10-26 | R1 | 0.90 | biosample.attribute:collection_date | 2015-10-26 |
| SAMN07583764 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:MO,St.Louis |
| SAMN07583764 | health_condition | healthy_control | R2 | 0.80 | paper.supp.41467_2024_53829_MOESM3_ESM.xlsx[Sheet1!cohort] | healthy |
| SAMN07583764 | health_condition_detail | healthy | R2 | 0.85 | paper.supp.41467_2024_53829_MOESM3_ESM.xlsx[Sheet1!cohort] | healthy |
| SAMN07583766 | health_condition_detail | mixed_case_control: recurrent urinary tract infection cases vs controls | R4 | 0.40 | paper.abstract | women with and without history of rUTI |
| SAMN07583764 | location_locality | St. Louis | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:MO,St.Louis |
| SAMN07583764 | location_region | Missouri | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:MO,St.Louis |
| SAMN07583764 | sex | female | R3 | 0.70 | paper.fulltext.methods | This study recruited only women |
| SAMN07583764 | subject_id | UMB01 | R1 | 0.70 | sample.name_rule:alias | UMB01_00 |
| SAMN07583764 | timepoint_label | 00 | R1 | 0.70 | sample.name_rule:alias | UMB01_00 |
| SAMN07583894 | timepoint_label | 2 | R2 | 0.85 | paper.supp.13059_2022_2630_MOESM3_ESM.xlsx[UTI sample identifiers!Time point] | 2 |
Sequencing
721 runs over 422 samples · mean 3.18 Gbp per run (median 2.89 Gbp, total 2,292.34 Gbp; 721 runs with a base count) · layout PAIRED 713, SINGLE 8 · platform ILLUMINA 713, OXFORD_NANOPORE 8 · models HiSeq X Ten (390), Illumina NovaSeq 6000 (222), Illumina HiSeq 2500 (101), GridION (8) · 80% of runs with a Sandpiper profile · first public 2017-11-09 – 2024-06-15
Authors (70)
van Dijk LR first · Walker BJ · Straub TJ · Worby CJ · Grote A · Schreiber HL · Anyansi C · Pickering AJ · Hultgren SJ · Manson AL · Abeel T · Earl AM last · Bronson RA · Olson BS · Pinkner JS · Obernuefemann CLP · Muñoz VL · Paharik AE · Azimzadeh PN · Desjardins CA · Chou WC · Bergeron K · Chapman SB · Klim A · Hannan TJ · Hooton TM · Kau AL · Lai HH · Dodson KW · Choi J first · Thänert R · Reske KA · Nickel KB · Olsen MA · Hink T · Thänert A · Wallace MA · Wang B · Cass C · Barlet MH · Struttmann EL · Iqbal ZH · Sax SR · Fraser VJ · Baker AW · Foy KR · Williams B · Xu B · Capocci-Tolomeo P · Lautenbach E · Burnham CD · Dubberke ER · Dantas G · Kwon JH · CDC Prevention Epicenters Program last · Young MG first · Metsky HC · Gnirke A · Matranga C · Qu J · Villicana JB · Azimzadeh P · Kau A · Kim Y first · Acharya S · Alfonsetti D · Gromko Z · Gerber GK · Berger B · Gibson TE last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA400628.csv.gz (12.3 KB) · parquet (85.9 KB) — all 422 samples, every field with route and confidence · PRJNA400628_determinations.csv.gz (22.0 KB) — 3,106 evidence rows