Cultivation of skin, oral, and gut bacteria, Farmington USA
46 samples from Farmington, USA, used to cultivate dominant bacterial species and strains from skin, oral, and gut microbiota via a metagenomics- and mass spectrometry-informed cultivation pipeline. machine-written summary
46 samples · 46 runs · US · Age unknown · 2022 · 0.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 322 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8515726 |
| ○ 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 |
longitudinal — not resolved
4 of 6 people sampled more than once (18 samples; median 4, up to 5 per person).
Genera, mean relative abundance over 4 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 | 0 | 0% | ||||
| country | 46 | 100% | 46 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 46 | 100% | 46 | |||
| collection_date | 46 | 100% | 46 | |||
| detailed_location | 46 | 100% | ||||
| latitude | 46 | 100% | 46 | |||
| location_locality | 46 | 100% | 46 | |||
| location_region | 46 | 100% | 46 | |||
| longitude | 46 | 100% | 46 |
- Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota. 2021 PMID 34649516 PMC8515726 own_data
Archive description
Cultivation of dominant bacterial species and strains from human skin, oral, and gut microbiota
How this project entered the registry
Classified as human skin / oral cavity / gut / stool / other human site shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human oral metagenome”
- body site study.title · “human skin, oral, and gut microbiota”
- body site run.scientific_name · “human skin metagenome”
- body site sample.attr.isolation_source · “toeweb (n=5/46)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19840714 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN19840714 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Farmington |
| SAMN19840714 | latitude | 41.7334 | R1 | 0.90 | biosample.attribute:lat_lon | 41.7334221 N 72.794137 W |
| SAMN19840714 | location_locality | Farmington | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Farmington |
| SAMN19840714 | location_region | Connecticut | R1 | 0.60 | biosample.attribute:lat_lon | 41.7334221 N 72.794137 W |
| SAMN19840714 | longitude | -72.7941 | R1 | 0.90 | biosample.attribute:lat_lon | 41.7334221 N 72.794137 W |
| SAMN19840714 | subject_id | 1000 | R1 | 0.70 | sample.name_rule:sample_alias | 1000.MSR-1 |
Sequencing
46 runs over 46 samples · mean 0.73 Gbp per run (median 0.42 Gbp, total 33.46 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models Illumina HiSeq 2500 (46) · 11% of runs with a Sandpiper profile · first public 2022-04-29
Authors (15)
Fleming E first · Pabst V · Scholar Z · Xiong R · Voigt AY · Zhou W · Hoyt A · Hardy R · Peterson A · Beach R · Ondouah-Nzutchi Y · Dong J · Bateman L · Vernon SD · Oh J last
Downloads
PRJNA740337.csv.gz (2.0 KB) · parquet (71.0 KB) — all 46 samples, every field with route and confidence · PRJNA740337_determinations.csv.gz (2.8 KB) — 322 evidence rows