Gut/oral microbiome, ethnicity and diet, healthy US females
522 gut and oral metagenome samples from healthy Black and White adult female subjects in the USA, studying ethnicity-associated microbiome variation with a controlled vegetarian diet intervention, in a longitudinal design. machine-written summary
522 samples · 522 runs · US · Age unknown · 2021 · 2.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,366 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2,610 sample values (health condition, health condition detail, location locality, location site, sex) · PMC11986028, PMC9397868 |
| ○ 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 · 4-day controlled vegetarian diet intervention
“a 4-day controlled vegetarian diet intervention” — abstract:35998206 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
36 of 222 people sampled more than once (214 samples; median 6, up to 9 per person). Schedule stated by the source: “before, during, and after a 4-day diet intervention” (time origin: intervention_start); stated follow-up 9 d.
Genera, mean relative abundance over 272 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 | 522 | 100% | ||||
| country | 522 | 100% | 522 | |||
| health_condition | 522 | 100% | 522 | |||
| subject_id | 471 | 90% | 471 | |||
| collection_date | 522 | 100% | 522 | |||
| detailed_location | 522 | 100% | ||||
| health_condition_detail | 522 | 100% | 522 | |||
| latitude | 522 | 100% | 522 | |||
| location_locality | 522 | 100% | 522 | |||
| location_region | 522 | 100% | 522 | |||
| location_site | 522 | 100% | 522 | |||
| longitude | 522 | 100% | 522 | |||
| sex | 522 | 100% | 522 | |||
| timepoint_label | 285 | 55% | 285 |
- Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes. 2022 PMID 35998206 PMC9397868 own_data
- Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut. 2025 PMID 40210629 PMC11986028 unsure
Archive description
Oral and gut metagenomes from female subjects
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “Oral and gut metagenomes from female subjects”
- body site run.scientific_name · “feces metagenome(220)”
- body site run.scientific_name · “oral metagenome(71)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19188900 | collection_date | 2018/2019 | R1 | 0.90 | biosample.attribute:collection_date | 2018/2019 |
| SAMN19188900 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN19188900 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Healthy women (age 18 to 40 years |
| SAMN19188900 | health_condition_detail | Healthy women | R3 | 0.70 | paper.fulltext.methods | Healthy women (age 18 to 40 years |
| SAMN19188900 | latitude | 36.1486 | R1 | 0.90 | biosample.attribute:lat_lon | 36.1486 N 86.8050 W |
| SAMN19188900 | location_locality | Nashville | R3 | 0.70 | paper.fulltext.methods | recruited from the greater area of Nashville, Tennessee, USA |
| SAMN19188900 | location_region | Tennessee | R1 | 0.60 | biosample.attribute:lat_lon | 36.1486 N 86.8050 W |
| SAMN19188900 | location_site | Vanderbilt Center for Human Nutrition | R3 | 0.70 | paper.fulltext.methods | visit to the Vanderbilt Center for Human Nutrition |
| SAMN19188900 | longitude | -86.8050 | R1 | 0.90 | biosample.attribute:lat_lon | 36.1486 N 86.8050 W |
| SAMN19188900 | sex | female | R3 | 0.70 | paper.fulltext.methods | Thirty-eight female adult participants |
| SAMN19188938 | subject_id | mb01 | R1 | 0.85 | sample.attr.subject | mb01 |
| SAMN19188938 | timepoint_label | Before | R1 | 0.85 | biosample.attribute:stage | stage: Before |
Sequencing
522 runs over 522 samples · mean 3.02 Gbp per run (median 2.29 Gbp, total 1,574.17 Gbp; 522 runs with a base count) · layout PAIRED 522 · platform ILLUMINA 522 · models Illumina NovaSeq 6000 (522) · 61% of runs with a Sandpiper profile · first public 2021-05-18 – 2022-09-30
Authors (25)
Li J first · George Markowitz RH · Brooks AW · Mallott EK · Leigh BA · Olszewski T · Zare H · Bagheri M · Smith HM · Friese KA · Habibi I · Lawrence WM · Rost CL · Lédeczi · Eeds AM · Ferguson JF · Silver HJ · Bordenstein SR last · Park JW first · Yun YE · Cho JA · Yoon SI · In SA · Park EJ · Kim MS last
Downloads
PRJNA662107.csv.gz (13.8 KB) · parquet (89.7 KB) — all 522 samples, every field with route and confidence · PRJNA662107_determinations.csv.gz (30.9 KB) — 5,976 evidence rows