Elderly gut microbiome during probiotic intervention in USA
9 gut metagenome samples from healthy elderly adults in the USA, studying functional dynamics of the gut microbiome during a probiotic intervention study. machine-written summary
9 samples · 9 runs · US · Elderly · 2015 · 12.75 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 63 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 27 sample values (health condition, health condition detail, location locality) · PMC4453556 |
| ○ 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 |
intervention — arms not resolved
Probiotic (live microorganisms; single strain or mixture) design single_arm_before_after · population healthy_control · Probiotic consumption study in elderly subjects
“during probiotic consumption” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
3 of 3 people sampled more than once (9 samples; median 3, up to 3 per person) · follow-up median 56 d (max 56 d) · median interval between samples 28 d (time from timepoint labels). Schedule stated by the source: “Fecal samples at baseline (day 0), day 28 (after 28 days LGG consumption), and day 56 (1 month after stopping LGG)” (time origin: intervention_start); stated follow-up 56 d.
Each row is one person (3 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 6 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 | 9 | 100% | ||||
| country | 9 | 100% | 9 | |||
| health_condition | 9 | 100% | 9 | |||
| subject_id | 9 | 100% | 9 | |||
| collection_date | 9 | 100% | 9 | |||
| detailed_location | 9 | 100% | ||||
| health_condition_detail | 9 | 100% | 9 | |||
| latitude | 9 | 100% | 9 | |||
| location_locality | 9 | 100% | 9 | |||
| location_region | 9 | 100% | 9 | |||
| longitude | 9 | 100% | 9 | |||
| timepoint_label | 9 | 100% | 9 |
- Functional dynamics of the gut microbiome in elderly people during probiotic consumption. 2015 PMID 25873374 PMC4453556 own_data
Archive description
metagenomics samples from a probiotic study of the eldery.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
- body site study.title · “of the elderly gut microbiome during probiotic”
- life stage study.title · “dynamics of the elderly gut microbiome during”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04158616 | collection_date | 2011 | R1 | 0.90 | biosample.attribute:collection_date | 2011 |
| SAMN04158616 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN04158616 | health_condition | healthy_control | R3 | 0.70 | paper.body.methods_results | healthy elderly volunteers |
| SAMN04158616 | health_condition_detail | healthy elderly volunteers | R3 | 0.70 | paper.body.methods_results | healthy elderly volunteers |
| SAMN04158616 | latitude | 42.3601 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN04158616 | location_locality | Boston | R3 | 0.70 | paper.body.methods_results | recruited from the Boston area |
| SAMN04158616 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN04158616 | longitude | -71.0589 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3601 N 71.0589 W |
| SAMN04158616 | subject_id | 40870 | R1 | 0.70 | sample.name_rule:sample_reference | 40870B |
| SAMN04158616 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:sample_reference | 40870B |
Sequencing
9 runs over 9 samples · mean 16.75 Gbp per run (median 12.75 Gbp, total 150.71 Gbp; 9 runs with a base count) · layout PAIRED 9 · platform ILLUMINA 9 · models Illumina HiSeq 2000 (9) · 67% of runs with a Sandpiper profile · first public 2015-11-10
Authors (0)
No author record.
Downloads
PRJNA298362.csv.gz (1.2 KB) · parquet (70.8 KB) — all 9 samples, every field with route and confidence · PRJNA298362_determinations.csv.gz (1.4 KB) — 90 evidence rows