Female urogenital and rectal microbiomes in UTI symptoms, USA
Cross-sectional study of 83 samples from urogenital and rectal swab sites in females with UTI symptoms, collected in Maywood, IL, USA, including elderly and adult age groups. machine-written summary
83 samples · 83 runs · US · Elderly · 2023 · 1.67 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 910 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
20 of 20 people sampled more than once (82 samples; median 4, up to 6 per person) · follow-up median 1 d (max 1 d) · median interval between samples 1 d (time from collection dates).
Each row is one person (1 shown of 20); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 76 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 | 82 | 99% | ||||
| country | 83 | 100% | 83 | |||
| health_condition | 83 | 100% | 83 | |||
| subject_id | 82 | 99% | 82 | |||
| collection_date | 83 | 100% | 83 | |||
| detailed_location | 83 | 100% | ||||
| health_condition_detail | 83 | 100% | 83 | |||
| latitude | 83 | 100% | 83 | |||
| location_locality | 83 | 100% | 83 | |||
| location_region | 83 | 100% | 83 | |||
| longitude | 83 | 100% | 83 | |||
| age_at_collection_days | 82 | 99% | 82 | |||
| sex | 82 | 99% | 82 |
Archive description
This study is aimed at identifying the microbes in urogenital samples as well as a rectal swab of females with UTI symptoms.
How this project entered the registry
Classified as human vaginal / urogenital / gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “urogenital samples as well as a rectal swab”
- body site run.scientific_name · “urine metagenome”
- body site run.scientific_name · “feces metagenome”
- life stage sample.attr.host_age · “68 (n=51/83)”
- life stage sample.attr.host_age · “51 (n=31/83)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN37835371 | age_at_collection_days | 28854.8 | R1 | 0.70 | sample.attr.host_age | 79 |
| SAMN37753975 | collection_date | 2021-05-19 | R1 | 0.90 | biosample.attribute:collection_date | 2021-05-19 |
| SAMN37753975 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Maywood, IL |
| SAMN37753975 | health_condition | other_infection | R1 | 0.85 | biosample.attribute:urogenit_tract_disor | UTI |
| SAMN37753975 | health_condition_detail | UTI | R1 | 0.90 | sample.attr.urogenit_tract_disor | UTI |
| SAMN37753975 | latitude | 41.8600 | R1 | 0.90 | biosample.attribute:lat_lon | 41.86 N 87.84 W |
| SAMN37753975 | location_locality | Maywood | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Maywood, IL |
| SAMN37753975 | location_region | Illinois | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Maywood, IL |
| SAMN37753975 | longitude | -87.8400 | R1 | 0.90 | biosample.attribute:lat_lon | 41.86 N 87.84 W |
| SAMN37835371 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN37753975 | subject_id | Participant1 | R1 | 0.70 | sample.name_rule:alias | Participant1_Bladder_LB |
Sequencing
83 runs over 83 samples · mean 1.73 Gbp per run (median 1.67 Gbp, total 143.25 Gbp; 83 runs with a base count) · layout PAIRED 83 · platform ILLUMINA 83 · models NextSeq 2000 (83) · 94% of runs with a Sandpiper profile · first public 2023-10-22
Authors (0)
No author record.
Downloads
PRJNA1026631.csv.gz (3.3 KB) · parquet (74.6 KB) — all 83 samples, every field with route and confidence · PRJNA1026631_determinations.csv.gz (6.8 KB) — 910 evidence rows