Duodenal microbiome in obese vs healthy adults, Marseille
2 samples from adults in Marseille, France, comparing the duodenal microbiota of obese individuals and healthy controls, focusing on lipid and carbohydrate metabolism genes, in a case-control design. machine-written summary
2 samples · 10 runs · FR · Age unknown · 2015 · 0.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 16 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC4565581 |
| ○ 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 |
Genera, mean relative abundance over 2 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 | 2 | 100% | ||||
| country | 2 | 100% | 2 | |||
| health_condition | 2 | 100% | 2 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 2 | 100% | 2 | |||
| detailed_location | 2 | 100% | ||||
| health_condition_detail | 2 | 100% | 2 | |||
| latitude | 2 | 100% | 2 | |||
| location_locality | 2 | 100% | 2 | |||
| location_region | 2 | 100% | 2 | |||
| longitude | 2 | 100% | 2 |
- A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity. 2015 PMID 26356733 PMC4565581 own_data
Archive description
The goal of the sutdy was to compare the functionnal genes of the duodenal gut between obese and healthy individuals</p><p>, particulary the lipid and carbohydrate metabolism
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome(10)”
- body site study.title · “the duodenal gut microbiome from obese and healthy subjects”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN03801588 | collection_date | 2003 | R1 | 0.90 | biosample.attribute:collection_date | 2003 |
| SAMN03801588 | country | FR | R1 | 0.90 | sample.attr.geo_loc_name | France: Marseille |
| SAMN03801588 | health_condition | obesity | R1 | 0.85 | biosample.attribute:description | description: weight_gain |
| SAMN03801588 | health_condition_detail | weight_gain | R1 | 0.85 | biosample.attribute:description | description: weight_gain |
| SAMN03801588 | latitude | 43.2900 | R1 | 0.90 | biosample.attribute:lat_lon | 43.29 N 5.38 E |
| SAMN03801588 | location_locality | Marseille | R1 | 0.85 | biosample.attribute:geo_loc_name | France: Marseille |
| SAMN03801588 | location_region | Provence-Alpes-Cote d'Azur | R1 | 0.60 | biosample.attribute:lat_lon | 43.29 N 5.38 E |
| SAMN03801588 | longitude | 5.3800 | R1 | 0.90 | biosample.attribute:lat_lon | 43.29 N 5.38 E |
Sequencing
10 runs over 2 samples · mean 0.11 Gbp per run (median 0.11 Gbp, total 1.06 Gbp; 10 runs with a base count) · layout PAIRED 10 · platform ILLUMINA 10 · models Illumina MiSeq (10) · 40% of runs with a Sandpiper profile · first public 2015-07-07
Authors (10)
Angelakis E first · Armougom F · Carrière F · Bachar D · Laugier R · Lagier JC · Robert C · Michelle C · Henrissat B · Raoult D last
Downloads
PRJNA287878.csv.gz (982 B) · parquet (70.1 KB) — all 2 samples, every field with route and confidence · PRJNA287878_determinations.csv.gz (718 B) — 16 evidence rows