Fiber vs fermented food diet effects on gut microbiome, CA
115 samples from healthy adults in California, in a 17-week randomized, prospective study (n=18/arm) comparing high-fiber and high-fermented-food diet interventions on the gut microbiome and immune system. machine-written summary
115 samples · 126 runs · US · Adult · 2021 · 6.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,150 sample values (collection date, country, diet, diet detail, intervention, intervention detail, latitude, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 230 sample values (health condition, health condition detail) · PMC11279133 |
| ○ 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 randomized_controlled_trial · population healthy_control · 17-week high-fiber vs high-fermented-food diet arms
“plant-based fiber or fermented foods” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
35 of 36 people sampled more than once (114 samples; median 4, up to 4 per person). Schedule stated by the source: “Repeated fecal sampling across a 17-week randomized intervention; catalog shows 35/36 subjects with >=2 samples (115 samples, 36 subjects).”.
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 | 115 | 100% | ||||
| country | 115 | 100% | 115 | |||
| health_condition | 115 | 100% | 115 | |||
| subject_id | 115 | 100% | 115 | |||
| collection_date | 115 | 100% | 115 | |||
| detailed_location | 115 | 100% | ||||
| diet | 115 | 100% | 115 | |||
| diet_detail | 115 | 100% | 115 | |||
| health_condition_detail | 115 | 100% | 115 | |||
| intervention | 115 | 100% | 115 | |||
| intervention_detail | 115 | 100% | 115 | |||
| latitude | 115 | 100% | 115 | |||
| location_region | 115 | 100% | 115 | |||
| longitude | 115 | 100% | 115 |
- High Prevalence of Antibiotic Resistance in Traditionally Fermented Foods as a Critical Risk Factor for Host Gut Antibiotic Resistome. 2024 PMID 39065201 PMC11279133 own_data
- Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. 2024 PMID 38914826 PMC11841136 unsure
Archive description
Diet modulates the gut microbiome, which, in turn, can impact the immune system. Here, we determined how two microbiota-targeted dietary interventions, plant-based fiber or fermented foods, influence the human microbiome and immune system in healthy adults. Using a 17-week randomized, prospective study (n = 18/arm) combined with -omics measurements of microbiome and host, including extensive immune profiling, we found diet-specific effects. The high-fiber diet increased microbiome-encoded glycan-degrading CAZymes despite stable microbial community diversity. While Cytokine Response Score (primary outcome) was unchanged, three distinct immunological trajectories in high fiber-consumers corresponded to baseline microbiota diversity. Alternatively, the high-fermented food diet steadily increased microbiota diversity and decreased inflammatory markers. The data highlight how coupling dietary interventions to deep and longitudinal immune and microbiome profiling can provide individualized and population-wide insight. Fermented foods may be valuable in countering the decreased microbiome diversity and increased inflammation pervasive in industrialized society.
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.description · “Diet modulates the gut microbiome, which, in”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “system in healthy adults . Using a”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20031224 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN20031224 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: California |
| SAMN20031224 | diet | other_diet | R1 | 0.90 | biosample.attribute:host_diet | Fermented |
| SAMN20031224 | diet_detail | Fermented | R1 | 0.90 | biosample.attribute:host_diet | Fermented |
| SAMN20031224 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 39 healthy adult participants were recruited |
| SAMN20031224 | health_condition_detail | healthy adults | R3 | 0.70 | paper.fulltext.methods | 39 healthy adult participants were recruited |
| SAMN20031224 | intervention | diet_intervention | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Fermented |
| SAMN20031224 | intervention_detail | high fermented food diet arm | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Fermented |
| SAMN20031224 | latitude | 37.4275 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4275 N 122.1697 W |
| SAMN20031224 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: California |
| SAMN20031224 | longitude | -122.1697 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4275 N 122.1697 W |
| SAMN20031224 | subject_id | 8027 | R1 | 0.85 | sample.attr.host_subject_id | 8027 |
Sequencing
126 runs over 126 samples · mean 7.60 Gbp per run (median 6.51 Gbp, total 957.97 Gbp; 126 runs with a base count) · layout PAIRED 126 · platform ILLUMINA 126 · models Illumina NovaSeq 6000 (126) · 96% of runs with a Sandpiper profile · first public 2021-07-05
Authors (15)
Quinn-Bohmann N first · Wilmanski T · Sarmiento KR · Levy L · Lampe JW · Gurry T · Rappaport N · Ostrem EM · Venturelli OS · Diener C · Gibbons SM last · Li Y first · Fu S · Klein MS · Wang H last
Downloads
PRJNA743361.csv.gz (3.9 KB) · parquet (75.3 KB) — all 115 samples, every field with route and confidence · PRJNA743361_determinations.csv.gz (9.7 KB) — 1,380 evidence rows