Twin study, vegan vs omnivorous diet, microbiome, Palo Alto
129 gut metagenome samples from adult identical twins in Palo Alto, California, USA, in a randomized dietary intervention trial comparing vegan and omnivorous diets and their effects on gut microbiome, metabolome, and immune markers. machine-written summary
129 samples · 129 runs · US · Adult · 2024 · 11.84 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,061 sample values (age, collection date, country, diet, diet detail, family id, family role, intervention) |
| ○ Abstract / description | read; no usable statement |
| – 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design randomized_controlled_trial · Randomized vegan vs omnivorous diet in twin pairs
“randomized trial involving 21 pairs of identical twins” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinaltwins
44 of 44 people sampled more than once (129 samples; median 3, up to 3 per person) · follow-up median 59 d (max 3 mo) · median interval between samples 28 d (time from collection dates). Schedule stated by the source: “Three timepoints (timepoint 1, 2, 3) per participant during randomized dietary intervention trial; exact day offsets not stated in provided text.” (time origin: intervention_start).
Each row is one person (36 shown of 44); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
22 identical-twin pairs (one twin vegan, one omnivore diet) via participant_id prefix · 22 families with 44 sampled people, 44 twin sets.
twin · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 22 linked groups from explicit relations. 44 people in the project overall.
Families (22)
Genera, mean relative abundance over 119 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 | 129 | 100% | ||||
| country | 129 | 100% | 129 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 129 | 100% | 129 | |||
| age_at_collection_days | 129 | 100% | 129 | |||
| detailed_location | 129 | 100% | ||||
| diet | 129 | 100% | 129 | |||
| diet_detail | 129 | 100% | 129 | |||
| family_id | 129 | 100% | 129 | |||
| family_role | 129 | 100% | 129 | |||
| intervention | 129 | 100% | 129 | |||
| intervention_detail | 129 | 100% | 129 | |||
| latitude | 129 | 100% | 129 | |||
| location_locality | 129 | 100% | 129 | |||
| location_region | 129 | 100% | 129 | |||
| longitude | 129 | 100% | 129 | |||
| sex | 129 | 100% | 129 | |||
| timepoint_label | 129 | 100% | 129 | |||
| collection_date | 126 | 98% | 126 |
- A gut pathobiont regulates circulating glycine and host metabolism in a twin study comparing vegan and omnivorous diets 2025 own_data
Archive description
Metabolic diseases such as type 2 diabetes and obesity pose a significant global health burden. Plant-based diets, including vegan diets, are linked to favorable metabolic outcomes, yet the underlying mechanisms remain unclear. In a randomized trial involving 21 pairs of identical twins, we investigated the effects of vegan and omnivorous diets on the host metabolome, immune system, and gut microbiome. Vegan diets induced significant shifts in serum and stool metabolomes, cytokine profiles, and gut microbial composition. Notably, vegan diet subjects exhibited elevated serum glycine levels despite lower dietary glycine intake, linked to reduced abundance of the gut pathobiont Bilophila wadsworthia. Functional studies demonstrated that B. wadsworthia metabolizes glycine via the glycine reductase pathway and modulates host glycine availability. Removing B. wadsworthia from gnotobiotic mice elevated glycine levels and improved metabolic markers. These findings reveal a previously underappreciated mechanism by which the gut microbiota regulates host metabolic status through diet.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “A gut pathobiont regulates circulating”
- body site study.description · “immune system, and gut microbiome. Vegan diets”
- body site study.description · “significant shifts in serum and stool metabolomes,”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN45999988 | age_at_collection_days | 10738.4 | R1 | 0.70 | sample.attr.age | 29.4 |
| SAMN45999988 | collection_date | 2022-03-31 | R1 | 0.90 | biosample.attribute:collection_date | 2022-03-31 |
| SAMN45999988 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: California, Palo Alto |
| SAMN45999988 | diet | omnivore | R1 | 0.90 | biosample.attribute:treatment_grp | Omnivore |
| SAMN45999988 | diet_detail | Omnivore | R1 | 0.90 | biosample.attribute:treatment_grp | Omnivore |
| SAMN45999988 | family_id | 7002 | R1 | 0.70 | sample.name_rule:participant_id | participant_id: 70021 |
| SAMN45999988 | family_role | twin | R1 | 0.70 | sample.name_rule:participant_id | participant_id: 70021 |
| SAMN45999988 | intervention | diet_intervention | R1 | 0.90 | biosample.attribute:treatment_grp | treatment_grp: Omnivore |
| SAMN45999988 | intervention_detail | omnivorous diet arm | R1 | 0.90 | biosample.attribute:treatment_grp | treatment_grp: Omnivore |
| SAMN45999988 | latitude | 37.4360 | R1 | 0.90 | biosample.attribute:lat_lon | 37.436 N 122.176 W |
| SAMN45999988 | location_locality | Palo Alto | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: California, Palo Alto |
| SAMN45999988 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: California, Palo Alto |
| SAMN45999988 | longitude | -122.1760 | R1 | 0.90 | biosample.attribute:lat_lon | 37.436 N 122.176 W |
| SAMN45999988 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN45999988 | subject_id | 70021 | R1 | 0.85 | sample.attr.participant_id | 70021 |
| SAMN45999988 | timepoint_label | 1 | R1 | 0.85 | sample.attr.timepoint | 1 |
Sequencing
129 runs over 129 samples · mean 12.46 Gbp per run (median 11.84 Gbp, total 1,607.15 Gbp; 129 runs with a base count) · layout PAIRED 129 · platform ILLUMINA 129 · models Illumina NovaSeq 6000 (129) · 92% of runs with a Sandpiper profile · first public 2024-12-29
Authors (0)
No author record.
Downloads
PRJNA1203651.csv.gz (5.2 KB) · parquet (77.5 KB) — all 129 samples, every field with route and confidence · PRJNA1203651_determinations.csv.gz (14.1 KB) — 2,061 evidence rows