Healthy adult gut microbiome, Washington D.C.
8 fecal samples from healthy adults in Washington D.C., USA, used to build a reference healthy gut microbiome catalog and abundance profile; cross-sectional design. machine-written summary
8 samples · 24 runs · US · Adult · 2018 · 0.94 Gbp / sample · cohort Baseline human gut microbiota profile in healthy p
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 77 sample values (age, bmi, collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC6738582 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 16 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
sex: sequence archive and GMrepo disagree for 3 samples (e.g. male vs female) — withheld.
The sources disagree on 3 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (3)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN09839340 | sex | male (sequence archive) | female (GMrepo) | withheld: neither value published |
| SAMN09839345 | sex | female (sequence archive) | male (GMrepo) | withheld: neither value published |
| SAMN09839346 | sex | female (sequence archive) | male (GMrepo) | withheld: neither value published |
longitudinal — not resolved
Schedule stated by the source: “Baseline visit followed by two follow-up visits, all within the same week; library_name suffixes (-1,-2,-3) correspond to the three visits per subject.” (time origin: enrolment).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 8 | 100% | ||||
| country | 8 | 100% | 8 | |||
| health_condition | 8 | 100% | 8 | |||
| subject_id | 8 | 100% | 8 | |||
| age_at_collection_days | 8 | 100% | 8 | |||
| bmi | 8 | 100% | 8 | |||
| collection_date | 8 | 100% | 8 | |||
| detailed_location | 8 | 100% | ||||
| health_condition_detail | 8 | 100% | 8 | |||
| latitude | 8 | 100% | 8 | |||
| location_locality | 8 | 100% | 8 | |||
| location_region | 8 | 100% | 8 | |||
| longitude | 8 | 100% | 8 | |||
| sex | 5 | 62% | 5 |
- Baseline human gut microbiota profile in healthy people and standard reporting template. 2019 PMID 31509535 PMC6738582 unsure
Archive description
The goal of this study is to characterize and to compare the bacterial species in the digestive system with diet, physical activity, and lifestyle practices, as well as metabolic markers such as glucose levels.This study consists of a baseline visit and two follow up visits within the same week. At the baseline visit, a fasted blood sample was collected to measure glucose levels, blood cholesterol, and other standard metabolic markers. Research staff also obtained satandard anthropometric measurements (e.g. height, weight, waist circumference)
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site study.title · “healthy human gut metagenomics”
- life stage sample.attr.host_age · “21.03 (n=6/8)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09839340 | age_at_collection_days | 7792.0 | R1 | 0.85 | sample.attr.host_age | 21.42 |
| SAMN09839340 | bmi | 22.95 | R1 | 0.90 | sample.attr.host_body_mass_index | 22.95 |
| SAMN09839340 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN09839340 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Washington D.C. |
| SAMN09839340 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN09839340 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN09839340 | latitude | 38.9021 | R1 | 0.90 | biosample.attribute:lat_lon | 38.902096 N 77.051046 W |
| SAMN09839340 | location_locality | Washington | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Washington D.C. |
| SAMN09839340 | location_region | Washington, D.C. | R1 | 0.60 | biosample.attribute:lat_lon | 38.902096 N 77.051046 W |
| SAMN09839340 | longitude | -77.0510 | R1 | 0.90 | biosample.attribute:lat_lon | 38.902096 N 77.051046 W |
| SAMN09839341 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN09839340 | subject_id | 1 | R1 | 0.85 | sample.attr.host_subject_id | 1 |
Sequencing
24 runs over 8 samples · mean 0.28 Gbp per run (median 0.30 Gbp, total 6.70 Gbp; 24 runs with a base count) · layout PAIRED 24 · platform ILLUMINA 24 · models Illumina MiSeq (24) · 0% of runs with a Sandpiper profile · first public 2018-08-22
Authors (40)
King CH first · Desai H · Sylvetsky AC · LoTempio J · Ayanyan S · Carrie J · Crandall KA · Fochtman BC · Gasparyan L · Gulzar N · Howell P · Issa N · Krampis K · Mishra L · Morizono H · Pisegna JR · Rao S · Ren Y · Simonyan V · Smith K · VedBrat S · Yao MD · Mazumder R last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA428202.csv.gz (1.2 KB) · parquet (71.1 KB) — all 8 samples, every field with route and confidence · PRJNA428202_determinations.csv.gz (1.6 KB) — 93 evidence rows