Underfeeding/overfeeding and vancomycin gut study, Phoenix
95 adult gut metagenome/16S rRNA samples from Phoenix, USA, from a two-phase inpatient intervention study comparing underfeeding versus overfeeding diets and oral vancomycin versus placebo. machine-written summary
95 samples · 95 runs · US · Adult · 2019 · 3.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 950 sample values (collection date, country, intervention, intervention detail, latitude, location locality, location region, longitude) |
| ○ 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 resolved
19 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy Controlled / prescribed diet or feeding regimen design randomized_controlled_trial · population healthy_control · Underfeeding vs overfeeding diet; oral vancomycin vs placebo
“underfeeding versus overfeeding) and antibiotic” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
19 of 19 people sampled more than once (95 samples; median 5, up to 5 per person) · follow-up median 18 d (max 20 d) · median interval between samples 3 d (time from collection dates). Schedule stated by the source: “Repeated sampling of 19 subjects across Phase I and Phase II of a two-phase crossover inpatient study (diet order UF_OF/OF_UF; timepoint_label distinct=2) with multiple numbered samples per subject (e” (time origin: intervention_start).
Each row is one person (19 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 85 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 | 95 | 100% | ||||
| country | 95 | 100% | 95 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 95 | 100% | 95 | |||
| collection_date | 95 | 100% | 95 | |||
| detailed_location | 95 | 100% | ||||
| intervention | 95 | 100% | 95 | |||
| intervention_detail | 95 | 100% | 95 | |||
| latitude | 95 | 100% | 95 | |||
| location_locality | 95 | 100% | 95 | |||
| location_region | 95 | 100% | 95 | |||
| longitude | 95 | 100% | 95 | |||
| timepoint_label | 95 | 100% | 95 |
- Diet-Related Alterations of Gut Bile Salt Hydrolases Determined Using a Metagenomic Analysis of the Human Microbiome. 2021 PMID 33915727 PMC8038126 unsure
Archive description
Metagenomic shotgun and V4 16S rRNA amplicon sequencing of human gut communities during dietary (underfeeding versus overfeeding) and antibiotic (vancomycin versus placebo) interventions in a two-phase inpatient study.
How this project entered the registry
Classified as human gut / stool / oral cavity 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 · “perturb the human gut microbiome and impair”
- body site study.description · “sequencing of human gut communities during dietary”
- body site study.title · “Underfeeding and oral vancomycin perturb the”
- 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 |
|---|---|---|---|---|---|---|
| SAMN13288211 | collection_date | 2014-03-22 | R1 | 0.90 | biosample.attribute:collection_date | 2014-03-22 |
| SAMN13288211 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Phoenix |
| SAMN13288211 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:host_diet | host_diet: WMD |
| SAMN13288211 | intervention_detail | weight-maintaining (eucaloric) baseline diet phase; assigned arm: underfeeding-then-overfeeding diet sequence arm | R1 | 0.80 | biosample.attribute:host_diet | host_diet: WMD |
| SAMN13288211 | latitude | 33.4900 | R1 | 0.90 | biosample.attribute:lat_lon | 33.49 N 112.05 W |
| SAMN13288211 | location_locality | Phoenix | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Phoenix |
| SAMN13288211 | location_region | Arizona | R1 | 0.60 | biosample.attribute:lat_lon | 33.49 N 112.05 W |
| SAMN13288211 | longitude | -112.0500 | R1 | 0.90 | biosample.attribute:lat_lon | 33.49 N 112.05 W |
| SAMN13288211 | subject_id | B | R1 | 0.85 | sample.attr.host_subject_id | B |
| SAMN13288241 | subject_id | M | R1 | 0.85 | biosample.attribute:host_subject_id | host_subject_id: M |
| SAMN13288211 | timepoint_label | Phase I | R1 | 0.85 | sample.attr.study_phase | Phase I |
Sequencing
95 runs over 95 samples · mean 3.46 Gbp per run (median 3.38 Gbp, total 328.50 Gbp; 95 runs with a base count) · layout PAIRED 95 · platform ILLUMINA 95 · models Illumina NovaSeq 6000 (95) · 89% of runs with a Sandpiper profile · first public 2019-11-20
Authors (14)
Jia B first · Park D · Chun BH · Hahn Y · Jeon CO last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · van Sinderen D
Downloads
PRJNA589622.csv.gz (3.9 KB) · parquet (75.1 KB) — all 95 samples, every field with route and confidence · PRJNA589622_determinations.csv.gz (7.1 KB) — 950 evidence rows