In vitro colonic fermentation of elderly gut microbiota
29 samples from Switzerland, derived from immobilized fecal microbiota of an elderly donor run in continuous colonic fermentation models (a three-stage model and the PolyFermS platform) simulating elderly gut fermentation. machine-written summary
29 samples · 29 runs · CH · Elderly · 2015 · 3.9 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 174 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 116 sample values (antibiotic exposure, health condition, health condition detail, sex) · PMC4641611 |
| ○ 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
2 of 2 people sampled more than once (29 samples; median 14, up to 16 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 29 | 100% | ||||
| country | 29 | 100% | 29 | |||
| health_condition | 29 | 100% | 29 | |||
| subject_id | 29 | 100% | 29 | |||
| antibiotic_exposure | 29 | 100% | 29 | |||
| collection_date | 29 | 100% | 29 | |||
| detailed_location | 29 | 100% | ||||
| health_condition_detail | 29 | 100% | 29 | |||
| latitude | 29 | 100% | 29 | |||
| location_region | 29 | 100% | 29 | |||
| longitude | 29 | 100% | 29 | |||
| sex | 29 | 100% | 29 |
- Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon. 2015 PMID 26559530 PMC4641611 own_data
Archive description
To study the microbiota of elderly using an intestinal fermentation model
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
- life stage study.description · “microbiota of elderly using an intestinal fermentation model”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN03294785 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | did not receive antibiotic treatment for at least three months |
| SAMN03294785 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMN03294785 | country | CH | R1 | 0.90 | sample.attr.geo_loc_name | Switzerland |
| SAMN03294785 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Fecal samples were collected from three healthy women |
| SAMN03294785 | health_condition_detail | healthy women | R3 | 0.70 | paper.fulltext.methods | Fecal samples were collected from three healthy women |
| SAMN03294785 | latitude | 47.3764 | R1 | 0.90 | biosample.attribute:lat_lon | 47.3764 N 8.5481 E |
| SAMN03294785 | location_region | Zurich | R1 | 0.60 | biosample.attribute:lat_lon | 47.3764 N 8.5481 E |
| SAMN03294785 | longitude | 8.5481 | R1 | 0.90 | biosample.attribute:lat_lon | 47.3764 N 8.5481 E |
| SAMN03294785 | sex | female | R3 | 0.70 | paper.fulltext.methods | Fecal samples were collected from three healthy women |
| SAMN03294785 | subject_id | F2 | R1 | 0.70 | sample.name_rule:alias | F2-F |
Sequencing
29 runs over 29 samples · mean 4.1 Mbp per run (median 3.9 Mbp, total 0.12 Gbp; 29 runs with a base count) · layout SINGLE 29 · platform LS454 29 · models 454 GS FLX Titanium (29) · 0% of runs with a Sandpiper profile · first public 2015-08-29
Authors (6)
Fehlbaum S first · Chassard C · Haug MC · Fourmestraux C · Derrien M · Lacroix C last
Downloads
PRJNA273574.csv.gz (1.4 KB) · parquet (70.9 KB) — all 29 samples, every field with route and confidence · PRJNA273574_determinations.csv.gz (2.4 KB) — 290 evidence rows