7-day homogeneous diet and gut microbiome, USA
105 samples from healthy adults in California, USA, studying a 7-day homogeneous average American diet intervention to assess interindividual variation in gut microbiome-dependent metabolites; intervention design. machine-written summary
105 samples · 105 runs · US · Adult · 2022 · 2.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 735 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 210 sample values (health condition, health condition detail) · PMC9296065 |
| ○ 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 design single_arm_before_after · population healthy_control · 7-day homogeneous average American diet in healthy individuals
“7-day homogeneous average American diet to standardize” — abstract:35643079 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
21 of 21 people sampled more than once (105 samples; median 5, up to 5 per person). Schedule stated by the source: “105 samples from 21 subjects across 5 distinct timepoints during/around a 7-day homogeneous diet intervention” (time origin: intervention/treatment start); stated follow-up 7 d.
Genera, mean relative abundance over 103 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 | 105 | 100% | ||||
| country | 105 | 100% | 105 | |||
| health_condition | 105 | 100% | 105 | |||
| subject_id | 105 | 100% | 105 | |||
| collection_date | 105 | 100% | 105 | |||
| detailed_location | 105 | 100% | ||||
| health_condition_detail | 105 | 100% | 105 | |||
| latitude | 105 | 100% | 105 | |||
| location_region | 105 | 100% | 105 | |||
| longitude | 105 | 100% | 105 | |||
| timepoint_label | 105 | 100% | 105 |
- Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes. 2022 PMID 35643079 PMC9296065 own_data
Archive description
Metabolism of dietary compounds by the gut microbiota generates a vast array of microbiome-dependent metabolites (MDMs), which are highly variable between individuals. The uremic MDMs (uMDMs) phenylacetylglutamine (PAG), p-cresol sulfate (PCS) and indoxyl sulfate (IS) accumulate during renal failure and are associated with poor outcomes. Targeted dietary interventions may reduce toxic MDMs generation however, it is unclear if interindividual differences in diet or gut microbiome dominantly contribute to MDM variance. Here we use a 7-day homogeneous average American diet to standardize dietary precursor availability in 21 healthy individuals. Notably, the coefficient of variation in three uMDMs of interest, PAG, PCS, and IS (primary outcome), did not significantly decrease. The majority of circulating MDMs maintained variation despite identical diets. These results highlight the highly personalized profile of MDMs and limited contribution of short-term dietary heterogeneity, suggesting that dietary modification may need to be paired with microbial therapies to control MDM profiles.
How this project entered the registry
Classified as human gut / stool 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 · “variation in human gut microbiomes and metabolomes”
- body site study.description · “compounds by the gut microbiota generates a”
- 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 |
|---|---|---|---|---|---|---|
| SAMN22794508 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN22794508 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: California |
| SAMN22794508 | health_condition | healthy_control | R3 | 0.60 | paper.fulltext.results | We enrolled healthy volunteers with diverse habitual diets |
| SAMN22794508 | health_condition_detail | healthy volunteers with diverse habitual diets | R3 | 0.60 | paper.fulltext.results | We enrolled healthy volunteers with diverse habitual diets |
| SAMN22794508 | latitude | 37.4275 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4275 N 122.1697 W |
| SAMN22794508 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: California |
| SAMN22794508 | longitude | -122.1697 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4275 N 122.1697 W |
| SAMN22794508 | subject_id | 02 | R1 | 0.70 | sample.name_rule:sample_alias | MISO1-S02-1_S2_R1 |
| SAMN22794508 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:sample_alias | MISO1-S02-1_S2_R1 |
Sequencing
105 runs over 105 samples · mean 2.35 Gbp per run (median 2.18 Gbp, total 247.22 Gbp; 105 runs with a base count) · layout PAIRED 105 · platform ILLUMINA 105 · models Illumina NovaSeq 6000 (105) · 98% of runs with a Sandpiper profile · first public 2022-08-11 – 2022-09-25
Authors (10)
Guthrie L first · Spencer SP · Perelman D · Van Treuren W · Han S · Yu FB · Sonnenburg ED · Fischbach MA · Meyer TW · Sonnenburg JL last
Downloads
PRJNA776530.csv.gz (3.5 KB) · parquet (74.0 KB) — all 105 samples, every field with route and confidence · PRJNA776530_determinations.csv.gz (7.1 KB) — 945 evidence rows