Human gut metagenome survey, Russia, cross-sectional
Cross-sectional survey of 119 stool samples from human gut microbiome, collected across several locations in Russia, including Moscow, Saint-Petersburg, Omsk region, and Khakassia. machine-written summary
119 samples · 127 runs · RU · Age unknown · 2015 · 1.59 Gbp / sample · cohort Human gut microbiota community structures in urban
One study deposited as 2 BioProjects (217 catalog samples together): PRJNA176385 · PRJNA243613 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 772 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 357 sample values (antibiotic exposure, health condition, health condition detail) · PMC3778515 |
| – 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 |
longitudinal — not resolvedfamilies — not resolved
14 of 46 people sampled more than once (28 samples; median 2, up to 2 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 119 | 100% | 119 | |||
| health_condition | 119 | 100% | 119 | |||
| subject_id | 60 | 50% | 60 | |||
| antibiotic_exposure | 119 | 100% | 119 | |||
| collection_date | 119 | 100% | 119 | |||
| detailed_location | 119 | 100% | ||||
| health_condition_detail | 119 | 100% | 119 | |||
| latitude | 119 | 100% | 119 | |||
| location_region | 119 | 100% | 119 | |||
| longitude | 119 | 100% | 119 | |||
| location_locality | 117 | 98% | 117 |
- Human gut microbiota community structures in urban and rural populations in Russia. 2013 PMID 24036685 PMC3778515 own_data
Archive description
Survey of human gut microbiome via metagenomics of stool samples
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Human stool Metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN02719534 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods | who did not receive anti-inflammatory or antimicrobial therapy for at least 3 months before inclusion |
| SAMN02719534 | collection_date | 2010-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2010-01-01 |
| SAMN02719534 | country | RU | R1 | 0.90 | sample.attr.geo_loc_name | Russia: Saint-Petersburg |
| SAMN02719534 | health_condition | healthy_control | R3 | 0.70 | paper.body.abstract | shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects |
| SAMN02719534 | health_condition_detail | healthy adult subjects, no intestinal dyspepsia symptoms | R3 | 0.70 | paper.body.abstract | shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects |
| SAMN02719534 | latitude | 59.9340 | R1 | 0.90 | biosample.attribute:lat_lon | 59.933962 N 30.347030 E |
| SAMN02719534 | location_locality | Saint Petersburg | R1 | 0.75 | biosample.attribute:geo_loc_name | Russia: Saint-Petersburg |
| SAMN02719534 | location_region | Saint Petersburg | R1 | 0.75 | biosample.attribute:geo_loc_name | Russia: Saint-Petersburg |
| SAMN02721266 | location_region | Omsk | R1 | 0.60 | biosample.attribute:lat_lon | 54.983918 N 73.381577 E |
| SAMN02719534 | longitude | 30.3470 | R1 | 0.90 | biosample.attribute:lat_lon | 59.933962 N 30.347030 E |
| SAMN02719534 | subject_id | Spb_105 | R1 | 0.70 | sample.name_rule:sample_alias | Spb_105 |
Sequencing
127 runs over 119 samples · mean 1.89 Gbp per run (median 1.59 Gbp, total 240.49 Gbp; 127 runs with a base count) · layout SINGLE 119, PAIRED 8 · platform ABI_SOLID 112, ION_TORRENT 15 · models AB SOLiD 4 System (112), Ion Torrent PGM (11), Ion Torrent Proton (4) · 0% of runs with a Sandpiper profile · first public 2015-04-04 – 2015-06-05
Authors (0)
No author record.
Downloads
PRJNA243613.csv.gz (4.2 KB) · parquet (75.9 KB) — all 119 samples, every field with route and confidence · PRJNA243613_determinations.csv.gz (9.5 KB) — 1,129 evidence rows