Yogurt and Oats Gut Microbiome Crossover Study, Germany
440 stool metagenome samples from healthy adult participants in Freiburg, Germany, in a randomized crossover trial testing daily yogurt versus yogurt plus rolled oats on gut microbiome composition. machine-written summary
440 samples · 440 runs · DE · Adult · 2025 · 6.89 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,706 sample values (age, bmi, collection date, country, intervention, intervention detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,762 sample values (antibiotic exposure, collection date, health condition, health condition detail, location site) · PMC13084677 |
| ○ 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 resolved
Controlled / prescribed diet or feeding regimen design crossover · population healthy_control · Daily 250g yogurt; then yogurt + 50g rolled oats, 4 weeks each
“250 g of yogurt daily followed by 250 g of yogurt with” — abstract:41687784 (study level; per-sample arms are in the intervention column below)
longitudinal
110 of 110 people sampled more than once (440 samples; median 4, up to 4 per person) · follow-up median 3 mo (max 11 mo) · median interval between samples 28 d (time from collection dates). Schedule stated by the source: “baseline (T1), after intervention 1 (T2), second baseline (T3), after intervention 2 (T4), each phase 4 weeks” (time origin: baseline); stated follow-up 4 mo.
Each row is one person (36 shown of 110); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 434 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 | 440 | 100% | ||||
| country | 440 | 100% | 440 | |||
| health_condition | 440 | 100% | 440 | |||
| subject_id | 440 | 100% | 440 | |||
| age_at_collection_days | 440 | 100% | 440 | |||
| antibiotic_exposure | 440 | 100% | 440 | |||
| collection_date | 440 | 100% | 438 | 2 | ||
| detailed_location | 440 | 100% | ||||
| health_condition_detail | 440 | 100% | 440 | |||
| intervention | 440 | 100% | 440 | |||
| intervention_detail | 440 | 100% | 440 | |||
| latitude | 440 | 100% | 440 | |||
| location_locality | 440 | 100% | 440 | |||
| location_region | 440 | 100% | 440 | |||
| location_site | 440 | 100% | 440 | |||
| longitude | 440 | 100% | 440 | |||
| sex | 440 | 100% | 440 | |||
| timepoint_label | 440 | 100% | 440 | |||
| bmi | 428 | 97% | 428 |
- Impact of Yogurt and Rolled Oats Consumption on the Gut Microbiome: A Randomized Crossover Study Displaying Individual Responses and General Resilience. 2026 PMID 41687784 PMC13084677 own_data
Archive description
We conducted a randomized controlled intervention study in which 110 healthy participants consumed 250 g of yogurt daily for four weeks in one intervention and 250 g of yogurt combined with 50 g of rolled oats in a second four-week intervention. Metagenomic sequencing and metabolomic analysis were conducted on stool samples, while health markers were assessed in the participants' blood. Here, we observed that yogurt consumption led to a transient increase in the abundance of yogurt bacteria in the gut microbiota of the study population. An additional 50 g of rolled oats caused a temporary slight homogenization of the microbial composition within and between participants which were mainly attributed to a relatively small sub-population with a Prevotella-predominant gut microbiota. No additional effects of yogurt or yogurt and rolled oats consumption on fecal SCFA concentrations and human health markers were identified. Functional analysis of the metagenomic data revealed fluctuations that were mostly attributable to the enrichment of yogurt-derived bacteria after both interventions. A healthy gut microbiota can withstand transient changes in diet without displaying drastic changes in gut microbial composition. The impact of diet is heavily dependent on an individual's baseline microbiome, underscoring the need for personalized dietary recommendations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “conducted on stool samples”
- life stage sample.attr.age_t0 · “27 (n=332/440)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN48395733 | age_at_collection_days | 7305.0 | R1 | 0.85 | sample.attr.age_t0 | 20 |
| SAMN48395737 | age_at_collection_days | 21915.0 | R1 | 0.85 | biosample.attribute:age_t0 | 60 |
| SAMN48395733 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | any antibiotics within the past 3 mo |
| SAMN48395733 | bmi | 19.3 | R1 | 0.70 | sample.attr.bmi_t0 | 19.3010649778022 |
| SAMN48395733 | collection_date | 2022-04-14 | R1 | 0.90 | biosample.attribute:collection_date | 2022-04-14 |
| SAMN48395921 | collection_date | 2020/2021 | R3 | 0.70 | paper.fulltext.methods | Recruiting and study started in 2020 and lasted until 2021 |
| SAMN48395733 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany:Freiburg |
| SAMN48395733 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 119 healthy volunteers were recruited |
| SAMN48395733 | health_condition_detail | 119 healthy volunteers | R3 | 0.70 | paper.fulltext.methods | 119 healthy volunteers were recruited |
| SAMN48395733 | intervention | synbiotic | R1 | 0.80 | biosample.attribute:intervention | intervention: After.YogurtRolledOat |
| SAMN48395733 | intervention_detail | after 4 weeks of yogurt plus rolled oats | R1 | 0.80 | biosample.attribute:intervention | intervention: After.YogurtRolledOat |
| SAMN48395733 | latitude | 48.0085 | R1 | 0.90 | biosample.attribute:lat_lon | 48.00853 N 7.83345 E |
| SAMN48395733 | location_locality | Freiburg | R1 | 0.85 | biosample.attribute:geo_loc_name | Germany:Freiburg |
| SAMN48395733 | location_region | Baden-Wuerttemberg | R1 | 0.60 | biosample.attribute:lat_lon | 48.00853 N 7.83345 E |
| SAMN48395733 | location_site | Institute for Prevention and Cancer Epidemiology, University of Freiburg | R3 | 0.70 | paper.fulltext.methods | Institute for Prevention and Cancer Epidemiology, Faculty of Medicine |
| SAMN48395733 | longitude | 7.8335 | R1 | 0.90 | biosample.attribute:lat_lon | 48.00853 N 7.83345 E |
| SAMN48395733 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN48395733 | subject_id | ID119 | R1 | 0.85 | sample.attr.participant_id | ID119 |
| SAMN48395733 | timepoint_label | T4 | R1 | 0.85 | sample.attr.timepoint | T4 |
Sequencing
440 runs over 440 samples · mean 7.10 Gbp per run (median 6.89 Gbp, total 3,121.84 Gbp; 440 runs with a base count) · layout PAIRED 440 · platform ILLUMINA 440 · models Illumina NovaSeq 6000 (440) · 99% of runs with a Sandpiper profile · first public 2025-05-13 – 2025-05-18
Authors (5)
Thriene K first · Stanislas V · Huang KD · Strowig T · Michels KB last
Downloads
PRJNA1258884.csv.gz (15.7 KB) · parquet (91.3 KB) — all 440 samples, every field with route and confidence · PRJNA1258884_determinations.csv.gz (46.6 KB) — 7,468 evidence rows