Gut microbiome vitamin K biosynthesis in elderly, Cork
74 gut microbiome samples from Cork, Ireland (mostly elderly, with 3 adult samples), shotgun sequenced to examine vitamin K biosynthesis. machine-written summary
74 samples · 74 runs · IE · Elderly · 2020 · 4.77 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 405 sample values (age, country, lifestyle, location region, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 74 sample values (antibiotic exposure) · PMC6885478 |
| ○ 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 67 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 | 74 | 100% | ||||
| country | 74 | 100% | 74 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 74 | 100% | 74 | |||
| age_at_collection_days | 74 | 100% | 74 | |||
| antibiotic_exposure | 74 | 100% | 74 | |||
| detailed_location | 74 | 100% | ||||
| location_region | 74 | 100% | 74 | |||
| sex | 74 | 100% | 74 | |||
| timepoint_label | 18 | 24% | 18 | |||
| lifestyle | 17 | 23% | 17 |
- Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults. 2019 PMID 31518386 PMC6885478 own_data
Archive description
Shotgun sequencing of the gut microbiome to look at vitamin K biosynthesis
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “gut microbiome to look at vitamin K”
- life stage sample.attr.age · “78 (n=72/74)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05891482 | age_at_collection_days | 29585.2 | R1 | 0.70 | sample.attr.age | 81 |
| SAMN05891482 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods_results | Subjects prescribed medication known to influence the gut microbiota and vitamin K status, including antibiotics and anticoagulants, were also excluded. |
| SAMN05891482 | country | IE | R1 | 0.90 | sample.attr.geo_loc_name | Ireland: Cork |
| SAMN05891484 | lifestyle | institutionalized | R1 | 0.85 | biosample.attribute:Strata | Longstay |
| SAMN05891482 | location_region | Cork | R1 | 0.85 | biosample.attribute:geo_loc_name | Ireland: Cork |
| SAMN05891482 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN05891482 | subject_id | EM142 | R1 | 0.70 | sample.name_rule:alias | EM142_T3 |
| SAMN05891482 | timepoint_label | T3 | R1 | 0.70 | sample.name_rule:alias | EM142_T3 |
Sequencing
74 runs over 74 samples · mean 4.71 Gbp per run (median 4.77 Gbp, total 348.74 Gbp; 74 runs with a base count) · layout PAIRED 74 · platform ILLUMINA 74 · models Illumina HiSeq 2000 (74) · 91% of runs with a Sandpiper profile · first public 2020-02-29
Authors (0)
No author record.
Downloads
PRJNA347511.csv.gz (3.0 KB) · parquet (73.5 KB) — all 74 samples, every field with route and confidence · PRJNA347511_determinations.csv.gz (4.5 KB) — 479 evidence rows