Diet and L. reuteri probiotic crossover trial, Edmonton, Canada
118 fecal samples from healthy adults in Edmonton, Alberta, Canada, from a randomized crossover trial testing a non-industrialized-type (Restore) diet combined with L. reuteri probiotic strains versus usual diet and placebo. machine-written summary
118 samples · 118 runs · CA · Adult · 2025 · 9.62 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 826 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ✓ Abstract / description | 236 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11380787 |
| ○ 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen Probiotic (live microorganisms; single strain or mixture) design crossover · population healthy_control · Non-industrialized high-fiber Restore diet vs usual diet; L. reuteri PB-W1 or DSM20016T vs placebo
“randomized crossover trial in healthy Canadian adults” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
30 of 30 people sampled more than once (118 samples; median 4, up to 4 per person) · follow-up median 2 mo (max 2 mo) · median interval between samples 31 d (time from collection months (month precision)).
Each row is one person (29 shown of 30); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 110 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 | 118 | 100% | ||||
| country | 118 | 100% | 118 | |||
| health_condition | 118 | 100% | 118 | |||
| subject_id | 118 | 100% | 118 | |||
| collection_date | 118 | 100% | 118 | |||
| detailed_location | 118 | 100% | ||||
| health_condition_detail | 118 | 100% | 118 | |||
| latitude | 118 | 100% | 118 | |||
| location_locality | 118 | 100% | 118 | |||
| location_region | 118 | 100% | 118 | |||
| longitude | 118 | 100% | 118 |
- Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples. 2024 PMID 39244633 PMC11380787 own_data
Archive description
Increased chronic disease prevalence in industrialized societies may be partially driven by western-style dietary patterns disrupting the gut microbiome. We explored the effects of a microbiome restoration strategy comprised of a non-industrialized-type (Restore) diet (providing ~45 grams/day dietary fiber) and a probiotic species Limosilactobacillus reuteri (a microbe rarely found in industrialized microbiomes) on gut microbiome ecology and host physiology. In a randomized crossover trial in healthy Canadian adults, 30 participants consumed the Restore diet or their usual diet for three weeks. Participants also consumed a single dose of either L. reuteri PB-W1 (an isolate from rural Papua New Guinea), L. reuteri DSM20016T (type strain of the species), or a placebo in each diet period.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “gut microbiome ecology and host physiology”
- life stage study.description · “healthy Canadian adults, 30 participants”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN45096721 | collection_date | 2019-02 | R1 | 0.90 | biosample.attribute:collection_date | 2019-02 |
| SAMN45096721 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada:Alberta,Edmonton |
| SAMN45096721 | health_condition | healthy_control | R4 | 0.50 | study.description | healthy Canadian adults |
| SAMN45096721 | health_condition_detail | All participants explicitly described as healthy. | R4 | 0.50 | study.description | healthy Canadian adults |
| SAMN45096721 | latitude | 53.5227 | R1 | 0.90 | biosample.attribute:lat_lon | 53.52273152 N 113.52139357 W |
| SAMN45096721 | location_locality | Edmonton | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada:Alberta,Edmonton |
| SAMN45096721 | location_region | Alberta | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada:Alberta,Edmonton |
| SAMN45096721 | longitude | -113.5214 | R1 | 0.90 | biosample.attribute:lat_lon | 53.52273152 N 113.52139357 W |
| SAMN45096721 | subject_id | 01 | R1 | 0.70 | sample.name_rule:alias | RW_01_Day0_P1 |
Sequencing
118 runs over 118 samples · mean 10.37 Gbp per run (median 9.62 Gbp, total 1,223.29 Gbp; 118 runs with a base count) · layout PAIRED 118 · platform ILLUMINA 118 · models Illumina NovaSeq 6000 (118) · 93% of runs with a Sandpiper profile · first public 2025-01-29
Downloads
PRJNA1000186.csv.gz (4.0 KB) · parquet (74.9 KB) — all 118 samples, every field with route and confidence · PRJNA1000186_determinations.csv.gz (7.5 KB) — 1,062 evidence rows