Gut microbiota and MDRO colonisation in nursing home residents
12 faecal samples from elderly residents of a nursing home in the Netherlands, studied longitudinally for colonisation with multidrug-resistant organisms and gut microbiota composition. machine-written summary
12 samples · 12 runs · NL · Elderly · 2020 · 0.75 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 68 sample values (collection date, country, latitude, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 24 sample values (lifestyle, lifestyle detail) · PMC8028076 |
| ○ 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 |
longitudinalcare home — not resolved
5 of 5 people sampled more than once (10 samples; median 2, up to 2 per person) · follow-up median 4 mo (max 4 mo) · median interval between samples 4 mo (time from collection dates). Schedule stated by the source: “four time points at 2-month intervals (October 2016-April 2017)” (time origin: enrolment); stated follow-up 6 mo.
Each row is one person (5 shown); dots are samples at days since that person's first sample.
5 residents of one Dutch nursing home (8 wards; ward per resident not given), 2 samples each.
Genera, mean relative abundance over 1 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 | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 10 | 83% | 10 | |||
| collection_date | 12 | 100% | 12 | |||
| latitude | 12 | 100% | 12 | |||
| lifestyle | 12 | 100% | 12 | |||
| lifestyle_detail | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 | |||
| timepoint_label | 10 | 83% | 10 |
- Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home. 2021 PMID 33827686 PMC8028076 own_data
Archive description
To be included
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 · “MDROs and gut microbiota in a”
- life stage study.title · “microbiota in a nursing home”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6796758 | collection_date | 2016-12-20 | R1 | 0.90 | biosample.attribute:collection_date | 2016-12-20 |
| SAMEA6796758 | country | NL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Netherlands |
| SAMEA6796758 | latitude | 52.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52 4,4931 |
| SAMEA6796758 | lifestyle | institutionalized | R3 | 0.70 | paper.fulltext.methods | residents of a nursing home in the Netherlands |
| SAMEA6796758 | lifestyle_detail | nursing home residents | R3 | 0.70 | paper.fulltext.methods | residents of a nursing home in the Netherlands |
| SAMEA6796758 | longitude | 4.4931 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52 4,4931 |
| SAMEA6796758 | subject_id | L001 | R1 | 0.70 | sample.name_rule:attr.description | Feces at time point 2 L001 |
| SAMEA6796758 | timepoint_label | 2 | R1 | 0.70 | sample.name_rule:attr.description | Feces at time point 2 L001 |
Sequencing
12 runs over 12 samples · mean 0.74 Gbp per run (median 0.75 Gbp, total 8.92 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina NovaSeq 6000 (12) · 8% of runs with a Sandpiper profile · first public 2020-07-14
Authors (11)
Ducarmon QR first · Terveer EM · Nooij S · Bloem MN · Vendrik KEW · Caljouw MAA · Sanders IMJG · van Dorp SM · Wong MC · Zwittink RD · Kuijper EJ last
Downloads
PRJEB37898.csv.gz (1.3 KB) · parquet (70.5 KB) — all 12 samples, every field with route and confidence · PRJEB37898_determinations.csv.gz (1.3 KB) — 92 evidence rows