Diet & antibiotic intervention on adult gut microbiome
474 samples from adults in Philadelphia, PA, studying effects of diet (vegan, omnivore, or fiber-free enteral nutrition) and an antibiotic-based microbiota depletion intervention on the gut microbiome and metabolome, in a longitudinal intervention design. machine-written summary
474 samples · 474 runs · US · Adult · 2020 · 1.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 7,442 sample values (age, antibiotic exposure, bmi, collection date, country, diet, diet detail, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10421625, PMC11060737, PMC11657513, PMC13362426, PMC8022197 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 20 sample values (bmi) · from MicrobiomeDB (VEuPathDB) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
Antibiotic given as the study intervention (incl. eradication therapy Controlled / prescribed diet or feeding regimen design single_arm_before_after · population healthy_control · Vegan, omnivore, or fiber-free EEN diet with antibiotic microbiota depletion, longitudinal
“vegan, omnivore, and a synthetic enteral nutrition” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
30 of 30 people sampled more than once (434 samples; median 15, up to 17 per person). Schedule stated by the source: “Daily fecal samples, 15 days: dietary d1-5, antibiotic/PEG purge d6-8, recovery d9-15 (pre/post-antibiotic sampling)” (time origin: enrolment); stated follow-up 15 d.
Genera, mean relative abundance over 355 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 | 474 | 100% | ||||
| country | 474 | 100% | 474 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 434 | 92% | 434 | |||
| collection_date | 474 | 100% | 474 | |||
| detailed_location | 474 | 100% | ||||
| health_condition_detail | 474 | 100% | 474 | |||
| latitude | 474 | 100% | 474 | |||
| location_locality | 474 | 100% | 474 | |||
| location_region | 474 | 100% | 474 | |||
| longitude | 474 | 100% | 474 | |||
| bmi | 434 | 92% | 414 | 20 | ||
| diet | 434 | 92% | 434 | |||
| diet_detail | 434 | 92% | 434 | |||
| intervention | 434 | 92% | 434 | |||
| intervention_detail | 434 | 92% | 434 | |||
| timepoint_label | 434 | 92% | 434 | |||
| age_at_collection_days | 414 | 87% | 414 | |||
| antibiotic_exposure | 414 | 87% | 414 | |||
| lifestyle | 139 | 29% | 139 | |||
| lifestyle_detail | 139 | 29% | 139 |
- Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. 2021 PMID 33440171 PMC8022197 own_data
- A widely distributed gene cluster compensates for uricase loss in hominids. 2023 PMID 37541197 PMC10421625 own_data
- Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae. 2024 PMID 38512401 PMC11060737 own_data
- TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies. 2024 PMID 39696594 PMC11657513 own_data
- Extracting host-specific developmental signatures from longitudinal microbiome data. 2026 PMID 42406847 PMC13362426 own_data
Archive description
Gut microbiota metabolites may be important for health yet studies are lacking that broadly correlate the composition of the human gut microbiome with the production of fecal metabolites and their impact on the plasma metabolome. Since gut microbiota metabolites are influenced by diet, we studied the impact of three divergent diets, vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber, on the human gut microbiome and its metabolome in a longitudinal analysis that included a microbiota depletion intervention.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome(474)”
- body site study.title · “Human Gut Microbiome and its Metabolome”
- life stage sample.attr.host_age · “24 (n=402/474)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16701291 | age_at_collection_days | 7305.0 | R1 | 0.85 | sample.attr.host_age | 20 |
| SAMN16701291 | antibiotic_exposure | no | R1 | 0.80 | sample.attr.current_antibiotics | Pre Antibiotics |
| SAMN16701296 | antibiotic_exposure | yes | R1 | 0.90 | biosample_attr | Antibiotics Treatment |
| SAMN16701291 | bmi | 21.3 | R1 | 0.90 | sample.attr.host_body_mass_index | 21.3 |
| SAMN16701743 | bmi | 21.3 | R2 | 0.75 | external.microbiomedb source | BMI: 21.3 |
| SAMN16701291 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN16701291 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Philadelphia, PA |
| SAMN16701291 | diet | vegan | R1 | 0.90 | biosample.attribute:host_diet | Vegan |
| SAMN16701291 | diet_detail | Vegan | R1 | 0.90 | biosample.attribute:host_diet | Vegan |
| SAMN16701291 | health_condition_detail | iscontrol: no | R1 | 0.85 | sample.attr.iscontrol | False |
| SAMN16701291 | intervention | diet_intervention | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Vegan |
| SAMN16701291 | intervention_detail | assigned vegan diet | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Vegan |
| SAMN16701291 | latitude | 39.9560 | R1 | 0.90 | biosample.attribute:lat_lon | 39.956 N 75.193 W |
| SAMN16701291 | lifestyle | vegetarian_or_vegan | R1 | 0.85 | biosample.attribute:host_diet | Vegan |
| SAMN16701291 | lifestyle_detail | Vegan | R1 | 0.85 | biosample.attribute:host_diet | Vegan |
| SAMN16701291 | location_locality | Philadelphia | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Philadelphia, PA |
| SAMN16701291 | location_region | Pennsylvania | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Philadelphia, PA |
| SAMN16701291 | longitude | -75.1930 | R1 | 0.90 | biosample.attribute:lat_lon | 39.956 N 75.193 W |
| SAMN16701291 | subject_id | 9002 | R1 | 0.85 | sample.attr.host_subject_id | 9002 |
| SAMN16701291 | timepoint_label | 1 | R1 | 0.85 | sample.attr.study_day | 1 |
Sequencing
474 runs over 474 samples · mean 1.71 Gbp per run (median 1.96 Gbp, total 811.43 Gbp; 474 runs with a base count) · layout PAIRED 474 · platform ILLUMINA 474 · models Illumina HiSeq 2500 (474) · 75% of runs with a Sandpiper profile · first public 2020-11-08 – 2020-11-09
Authors (61)
Tanes C first · Bittinger K · Gao Y · Friedman ES · Nessel L · Paladhi UR · Chau L · Panfen E · Fischbach MA · Braun J · Xavier RJ · Clish CB · Li H · Bushman FD · Lewis JD · Wu GD last · Liu Y first · Jarman JB · Low YS · Augustijn HE · Huang S · Chen H · DeFeo ME · Sekiba K · Hou BH · Meng X · Weakley AM · Cabrera AV · Zhou Z · van Wezel G · Medema MH · Ganesan C · Pao AC · Gombar S · Dodd D last · Hecht AL first · Harling LC · Lee J · Firrman J · Hao F · Tu V · Liu L · Patterson AD · Goulian M · Shi P first · Martino C · Han R · Janssen S · Buck G · Serrano M · Owzar K · Knight R · Shenhav L · Zhang AR last · Erdős B first · Chatzis C · Thorsen J · Stokholm J · Smilde AK · Rasmussen MA · Acar E last
Downloads
PRJNA675301.csv.gz (13.4 KB) · parquet (89.0 KB) — all 474 samples, every field with route and confidence · PRJNA675301_determinations.csv.gz (47.7 KB) — 7,462 evidence rows