Home › Studies › PRJNA528960
PRJNA528960 SRP253683

Gut microbiome in cranberry trial for recurrent UTI, USA

Metagenomic sequencing of stool Metagenome

133 stool samples from USA participants in a recurrent urinary tract infection trial, comparing gut microbiota between cranberry beverage and placebo dietary supplement intervention arms. machine-written summary

133 samples · 262 runs · US · Age unknown · 2020 · 9.25 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 203○Abstract / description✓Full text 133✓Supplementary tables 393–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive203 sample values (country, health condition, health condition detail)
○ Abstract / descriptionread; no usable statement
✓ Full text133 sample values (sex) · PMC7890861
✓ Supplementary tables393 sample values (intervention, subject id, timepoint)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention · arms resolved

RNon-microbial dietary supplement (vitamins: 35 people · 64 samplessupplement 35 people · 64 samplesPlacebo / sham arm (sample level only): 35 people · 67 samplesplacebo 35 people · 67 samples
randomised to parallel arms

Non-microbial dietary supplement (vitamins design randomized_controlled_trial · population other_disease · Daily cranberry beverage vs placebo for 24 weeks

“long-term daily cranberry consumption” — abstract:33596852 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 country
Age
unknown133
Condition
other_infection35
Sex
female133
Country
US133
Body site
primary133
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 14 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 62 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 57 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 9.25 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

54 of 70 people sampled more than once (115 samples; median 2, up to 4 per person) · follow-up median 6 mo (max 6 mo) · median interval between samples 6 mo (time from timepoint labels). Schedule stated by the source: “stool provided at the start (week 0) and end (week 24) of the study window” (time origin: intervention start); stated follow-up 6 mo.

01-00201-002: day 001-002: day 16801-00301-003: day 001-003: day 16801-00801-008: day 001-008: day 16801-01001-010: day 001-010: day 16801-02001-020: day 001-020: day 16801-02401-024: day 001-024: day 16801-02701-027: day 001-027: day 16801-02901-029: day 001-029: day 16801-03601-036: day 001-036: day 16801-03901-039: day 001-039: day 16802-00602-006: day 002-006: day 16802-00702-007: day 002-007: day 16802-00802-008: day 002-008: day 16802-01302-013: day 002-013: day 16802-01402-014: day 002-014: day 16802-01702-017: day 002-017: day 16802-01802-018: day 002-018: day 16802-02102-021: day 002-021: day 16802-02502-025: day 002-025: day 16802-02602-026: day 002-026: day 16802-03502-035: day 002-035: day 16802-03802-038: day 002-038: day 16802-04202-042: day 002-042: day 16802-04402-044: day 002-044: day 16802-05102-051: day 002-051: day 16804-00104-001: day 004-001: day 16804-01304-013: day 004-013: day 16804-01704-017: day 004-017: day 16804-01804-018: day 004-018: day 16804-02804-028: day 004-028: day 16804-03104-031: day 004-031: day 16807-00307-003: day 007-003: day 16807-00707-007: day 007-007: day 16807-01107-011: day 007-011: day 16807-01207-012: day 007-012: day 16809-00109-001: day 009-001: day 1680 d42 d3 mo4 mo6 mo

Each row is one person (36 shown of 54); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 15.3%Phocaeicola 7.6%Roseburia 6.3%Faecalibacterium 6.3%Alistipes 6.1%Prevotella 3.4%Bifidobacterium 2.6%Blautia_A 2.1%Parabacteroides 1.9%Lachnospira 1.8%Vescimonas 1.7%Gemmiger 1.7%not assigned to a genus 7.8%other genera 35.4%

Genera, mean relative abundance over 129 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country133 100%133
health_condition35 26%35
subject_id131 98%131
sex133 100%133
intervention131 98%131
timepoint_label131 98%131
health_condition_detail35 26%35
Papers (1)
  • Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. 2021 PMID 33596852 PMC7890861 own_data
Details
Archive description

Metagenomic sequencing of stool samples

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site study.title · “Metagenomic sequencing of stool Metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN11482917countryUSR10.90sample.attr.geo_loc_nameUSA
SAMN14002520health_conditionother_infectionR10.85biosample_attrUrinary Tract Infection
SAMN14002520health_condition_detailUrinary Tract InfectionR10.90sample.attr.host_diseaseUrinary Tract Infection
SAMN11482917interventionplaceboR20.80paper.supp.12866_2021_2106_MOESM4_ESM.txt[!Treatment]Placebo
SAMN11482917sexfemaleR30.70paper.fulltext.methodshealthy women with a history of rUTI
SAMN11482917subject_id01-002R20.85paper.supp.12866_2021_2106_MOESM4_ESM.txt[!Patient]CRNd00004-1 -> 01-002
SAMN11482917timepoint_labelBaselineR20.85paper.supp.12866_2021_2106_MOESM4_ESM.txt[!Visit]CRNd00004-1 -> Baseline
Sequencing

262 runs over 133 samples · mean 4.52 Gbp per run (median 3.30 Gbp, total 1,185.42 Gbp; 262 runs with a base count) · layout PAIRED 262 · platform ILLUMINA 262 · models HiSeq X Ten (131), Illumina HiSeq 2500 (131) · 87% of runs with a Sandpiper profile · first public 2020-04-14 – 2023-07-31

Authors (15)

Straub TJ first · Chou WC · Manson AL · Schreiber HL · Walker BJ · Desjardins CA · Chapman SB · Kaspar KL · Kahsai OJ · Traylor E · Dodson KW · Hullar MAJ · Hultgren SJ · Khoo C · Earl AM last

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

Downloads

PRJNA528960.csv.gz (4.6 KB) · parquet (75.2 KB) — all 133 samples, every field with route and confidence · PRJNA528960_determinations.csv.gz (5.1 KB) — 729 evidence rows

Samples (133 · every field this project has values for · hover a cell for its source)
Loading the sample table…