Resistant starch blend trial, San Diego adults
222 samples from adults in San Diego, CA, USA, from a randomized trial comparing doses of a resistant starch/fiber blend (potato starch, green banana flour, apple fiber) against a potato starch control, assessing GI symptoms and gut microbiome. machine-written summary
222 samples · 222 runs · US · Adult · 2022 · 1.15 Gbp / sample · cohort Contamination source modeling with SCRuB improves
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,094 sample values (age, antibiotic exposure, bmi, collection date, country, diet, diet detail, health condition) |
| ✓ Abstract / description | 166 sample values (health condition, health condition detail) |
| ✓ Full text | 50 sample values (antibiotic exposure, collection date) · PMC9559413 |
| ○ 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
Prebiotic / dietary fibre supplement design randomized_controlled_trial · population healthy_control · Resistant starch blend (potato, banana, apple fiber) vs potato starch control, escalating doses
“Resistant starch gut microbiome” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
41 of 64 people sampled more than once (199 samples; median 5, up to 5 per person) · follow-up median 36 d (max 44.4 y) · median interval between samples 36 d (time from age at collection). Schedule stated by the source: “assessed at 2, 4, and 6 weeks of dosing (6-week trial)” (time origin: intervention_start); stated follow-up 42 d.
Each row is one person (36 shown of 41); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 78 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 | 222 | 100% | ||||
| country | 222 | 100% | 222 | |||
| health_condition | 222 | 100% | 86 | 136 | ||
| subject_id | 222 | 100% | 222 | |||
| antibiotic_exposure | 222 | 100% | 192 | 30 | ||
| collection_date | 222 | 100% | 202 | 20 | ||
| detailed_location | 222 | 100% | ||||
| health_condition_detail | 222 | 100% | 192 | 30 | ||
| location_locality | 222 | 100% | 222 | |||
| location_region | 222 | 100% | 222 | |||
| age_at_collection_days | 201 | 91% | 201 | |||
| diet | 197 | 89% | 197 | |||
| diet_detail | 197 | 89% | 197 | |||
| smoking_status | 197 | 89% | 197 | |||
| sex | 196 | 88% | 196 | |||
| bmi | 193 | 87% | 193 | |||
| timepoint_label | 186 | 84% | 186 | |||
| medication | 75 | 34% | 75 | |||
| medication_detail | 65 | 29% | 65 | |||
| stool_consistency_bristol | 27 | 12% | 27 |
- The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps. 2022 PMID 36245486 PMC9559413 own_data
- Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. 2023 PMID 36928429 PMC10504420 unsure
Archive description
The gastrointestinal (GI) impact of resistant starch consumption depends on microbiomes, adherence, and various types and amounts of resistant starch. A randomized clinical trial with smart cap monitoring was used to evaluate the GI impact of a novel resistant starch blend (RSB) at varying doses. The study design randomized participants to a potato starch as a control or one of three arms ramping doses from 10 to 30 g /day over 6 weeks of RSB, a proprietary mixture of a different potato starch, green banana flour and apple fiber powder. The blend contained at least 50% resistant starch. Total short-chain fatty acids (SCFA) increased with increasing doses of the RSB. GI symptoms improved in all groups, and the increasing doses of RSB led to a decrease in the diarrhea score. Using an estimate of total consumption of RSB based on smart cap recordings of container openings and protocol-specified doses, we showed that a reduction in the sleep disturbance score was associated with higher RSB dose. The microbiome evaluation demonstrated that among the 16S sequences most associated with the consumption of the novel blend RSB, two belong to taxa of notable interest to human health: Faecalibacterium and Akkermansia.
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 run.scientific_name · “human gut metagenome”
- life stage sample.attr.life_stage · “Adult (n=200/222)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA12565662 | age_at_collection_days | 14281.3 | R1 | 0.90 | sample.attr.age_years | 39.1 |
| SAMEA12565662 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | I have not taken antibiotics in the past year. |
| SAMEA12565750 | antibiotic_exposure | yes | R1 | 0.80 | sample.attr.antibiotic_history | Month |
| SAMEA12565701 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | use of antibiotic, antiparasitic, or antifungal drugs |
| SAMEA12565662 | bmi | 28.2 | R1 | 0.90 | sample.attr.bmi | 28.2 |
| SAMEA12565662 | collection_date | 2020-03-18 | R1 | 0.85 | biosample.attribute:collection_timestamp | 2020-03-18T16:25:00 |
| SAMEA12565831 | collection_date | 2019-06/2020-12 | R3 | 0.70 | paper.fulltext.methods | clinical trial ran from June 2019 through December 2020 |
| SAMEA12565662 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:CA:San Diego |
| SAMEA12565662 | diet | omnivore | R1 | 0.90 | biosample.attribute:diet_type | Omnivore |
| SAMEA12565662 | diet_detail | Omnivore | R1 | 0.90 | biosample.attribute:diet_type | Omnivore |
| SAMEA12565669 | health_condition | neurological_psychiatric | R1 | 0.85 | biosample_attr | true |
| SAMEA12565662 | health_condition | healthy_control | R4 | 0.50 | study.description | randomized clinical trial with smart cap monitoring |
| SAMEA12565662 | health_condition_detail | I do not have this condition | R1 | 0.90 | sample.attr.clinical_condition | I do not have this condition |
| SAMEA12565715 | health_condition_detail | Randomized intervention trial evaluating resistant starch blend consumption. | R4 | 0.50 | study.description | randomized clinical trial with smart cap monitoring |
| SAMEA12565662 | location_locality | San Diego | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:CA:San Diego |
| SAMEA12565662 | location_region | California | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:CA:San Diego |
| SAMEA12565663 | medication | other_medication | R1 | 0.85 | biosample.attribute:vitamin_d_supplement_frequency | vitamin_d_supplement_frequency: Daily |
| SAMEA12565674 | medication | other_medication | R1 | 0.85 | biosample.attribute:vitamin_b_supplement_frequency;vitamin_d_supplement_frequency | vitamin_b_supplement_frequency: Daily; vitamin_d_supplement_frequency: Daily |
| SAMEA12565701 | medication | other_medication | R1 | 0.85 | biosample.attribute:vitamin_b_supplement_frequency | vitamin_b_supplement_frequency: Regularly (3-5 times/week) |
| SAMEA12565705 | medication | other_medication | R1 | 0.90 | biosample.attribute:acne_medication_otc | Yes |
| SAMEA12565663 | medication_detail | vitamin_d_supplement_frequency: Daily | R1 | 0.85 | biosample.attribute:vitamin_d_supplement_frequency | vitamin_d_supplement_frequency: Daily |
| SAMEA12565674 | medication_detail | vitamin_b_supplement_frequency: Daily; vitamin_d_supplement_frequency: Daily | R1 | 0.85 | biosample.attribute:vitamin_b_supplement_frequency;vitamin_d_supplement_frequency | vitamin_b_supplement_frequency: Daily; vitamin_d_supplement_frequency: Daily |
| SAMEA12565701 | medication_detail | vitamin_b_supplement_frequency: Regularly (3-5 times/week) | R1 | 0.85 | biosample.attribute:vitamin_b_supplement_frequency | vitamin_b_supplement_frequency: Regularly (3-5 times/week) |
| SAMEA12565662 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMEA12565662 | smoking_status | never | R1 | 0.90 | biosample.attribute:smoking_frequency | Never |
| SAMEA12565668 | stool_consistency_bristol | 5 | R1 | 0.90 | biosample.attribute:stool_consistency | 5 |
| SAMEA12565662 | subject_id | c453a6c6b56ef4609da05373ce79f814f852005653deb6c60a81558a9048f27c9f4157731c1291a06f8673988ac47d01826f64961e802b09ef4df744 | R1 | 0.85 | sample.attr.host_subject_id | c453a6c6b56ef4609da05373ce79f814f852005653deb6c60a81558a9048f27c9f4157731c1291a06f8673988ac47d01826f64961e802b09ef4df744 |
| SAMEA12565663 | timepoint_label | 1 | R1 | 0.85 | sample.attr.time_point | 1 |
Sequencing
222 runs over 222 samples · mean 1.77 Gbp per run (median 1.15 Gbp, total 392.07 Gbp; 222 runs with a base count) · layout PAIRED 222 · platform ILLUMINA 222 · models Illumina NovaSeq 6000 (222) · 35% of runs with a Sandpiper profile · first public 2022-01-26
Authors (22)
Hanes D first · Nowinski B · Lamb JJ · Larson IA · McDonald D · Knight R · Song SJ · Patno N last · Austin GI first · Park H · Meydan Y · Seeram D · Sezin T · Lou YC · Firek BA · Morowitz MJ · Banfield JF · Christiano AM · Pe'er I · Uhlemann AC · Shenhav L · Korem T last
Downloads
PRJEB50408.csv.gz (13.2 KB) · parquet (95.8 KB) — all 222 samples, every field with route and confidence · PRJEB50408_determinations.csv.gz (34.5 KB) — 3,310 evidence rows