ESBL-E gut microbiome in nursing home elderly, Nantes
144 fecal samples from elderly nursing home residents in Nantes, France, comparing ESBL-E carriers to non-carriers using shotgun metagenomics in a case-control design. machine-written summary
144 samples · 144 runs · FR · Age unknown · 2019 · 0.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 720 sample values (collection date, country, latitude, location locality, longitude) |
| ✓ Abstract / description | 144 sample values (lifestyle detail) |
| ✓ Full text | 288 sample values (lifestyle, subject id) · PMC7359458 |
| ○ 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 |
care home — not resolved
144 residents of two nursing homes (care-home setting); home per resident not deposited.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 144 | 100% | ||||
| country | 144 | 100% | 144 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 144 | 100% | 144 | |||
| collection_date | 144 | 100% | 144 | |||
| detailed_location | 144 | 100% | ||||
| latitude | 144 | 100% | 144 | |||
| lifestyle | 144 | 100% | 144 | |||
| lifestyle_detail | 144 | 100% | 144 | |||
| location_locality | 144 | 100% | 144 | |||
| longitude | 144 | 100% | 144 |
- Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases. 2020 PMID 32665016 PMC7359458 own_data
Archive description
Metagenomic exploration of ESBL-E carriers gut microbiome
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “ESBL-E carriers gut microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11356380 | collection_date | 2018-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2018-01-01 |
| SAMN11356380 | country | FR | R1 | 0.90 | sample.attr.geo_loc_name | France: Nantes |
| SAMN11356380 | latitude | 47.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 47.20 N 1.55 W |
| SAMN11356380 | lifestyle | institutionalized | R3 | 0.70 | paper.fulltext.methods | elderly residents from two public nursing homes |
| SAMN11356380 | lifestyle_detail | nursing home residents | R4 | 0.50 | paper.abstract | nursing home residents carrying Enterobacteria producing extended-spectrum |
| SAMN11356380 | location_locality | Nantes | R1 | 0.85 | biosample.attribute:geo_loc_name | France: Nantes |
| SAMN11356380 | longitude | -1.5500 | R1 | 0.90 | biosample.attribute:lat_lon | 47.20 N 1.55 W |
| SAMN11356380 | subject_id | SAMN11356380 | R3 | 0.75 | design.one_sample_per_subject:fulltext | This study was part of a point prevalence survey ... The study population consisted of 144 elderly residents |
Sequencing
144 runs over 144 samples · mean 0.20 Gbp per run (median 0.20 Gbp, total 29.12 Gbp; 144 runs with a base count) · layout SINGLE 144 · platform ILLUMINA 144 · models Illumina HiSeq 2500 (144) · 0% of runs with a Sandpiper profile · first public 2019-07-16 – 2019-07-17
Authors (19)
Le Bastard Q first · Chapelet G · Birgand G · Hillmann BM · Javaudin F · Hayatgheib N · Bourigault C · Bemer P · De Decker L · Batard E · Lepelletier D · Montassier E last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last
Downloads
PRJNA531316.csv.gz (4.5 KB) · parquet (76.3 KB) — all 144 samples, every field with route and confidence · PRJNA531316_determinations.csv.gz (7.1 KB) — 1,152 evidence rows