Gut microbiota in hospitalised elderly, Parma, Italy
15 fecal samples from hospitalised elderly patients in Parma, Italy, studied for gut microbiota composition in relation to C. difficile infection, polypharmacy, multimorbidity and frailty, using a case-control design. machine-written summary
15 samples · 15 runs · IT · Adult · 2016 · 0.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 45 sample values (collection date, country, location locality) |
| ✓ Abstract / description | 15 sample values (health condition detail) |
| ✓ Full text | 15 sample values (subject id) · PMC4863157, PMC5593887 |
| ○ 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
design observational_with_procedure
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 15 | 100% | ||||
| country | 15 | 100% | 15 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 15 | 100% | 15 | |||
| collection_date | 15 | 100% | 15 | |||
| detailed_location | 15 | 100% | ||||
| health_condition_detail | 15 | 100% | 15 | |||
| location_locality | 15 | 100% | 15 |
- Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. 2016 PMID 27166072 PMC4863157 own_data
- Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients. 2017 PMID 28894183 PMC5593887 own_data
- Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. 2018 PMID 29445826 PMC6132499 unsure
- PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. 2021 PMID 33597026 PMC7890817 unsure
- Functional profile of host microbiome indicates Clostridioides difficile infection. 2022 PMID 36289064 PMC9621045 unsure
Archive description
Fecal microbiota of hospitalised Elderlies with and without Peptoclostridium difficile infection
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Fecal microbiota of hospitalised”
- body site study.description · “Fecal microbiota of hospitalised”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04121056 | collection_date | 2015-01-01 | R1 | 0.90 | biosample.attribute:collection_date | 2015-01-01 |
| SAMN04121056 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy: parma |
| SAMN04121056 | health_condition_detail | mixed_case_control: CDI-positive patients vs CDI-negative subjects (with and without prior antibiotic exposure). | R4 | 0.50 | paper.abstract | CDI-positive (CDI group), 29 CDI-negative |
| SAMN04121056 | location_locality | Parma | R1 | 0.85 | biosample.attribute:geo_loc_name | Italy: parma |
| SAMN04121056 | subject_id | SAMN04121056 | R3 | 0.75 | design.one_sample_per_subject:fulltext | the cross-sectional study design did not allow to establish whether each of the detected alterations |
Sequencing
15 runs over 15 samples · mean 0.26 Gbp per run (median 0.27 Gbp, total 3.91 Gbp; 15 runs with a base count) · layout PAIRED 15 · platform ILLUMINA 15 · models Illumina MiSeq (15) · 0% of runs with a Sandpiper profile · first public 2016-10-07
Authors (37)
Milani C first · Ticinesi A · Gerritsen J · Nouvenne A · Lugli GA · Mancabelli L · Turroni F · Duranti S · Mangifesta M · Viappiani A · Ferrario C · Maggio M · Lauretani F · De Vos W · van Sinderen D · Meschi T · Ventura M last · Cabal A first · Jun SR · Jenjaroenpun P · Wanchai V · Nookaew I · Wongsurawat T · Burgess MJ · Kothari A · Wassenaar TM · Ussery DW last · de Nies L first · Lopes S · Busi SB · Galata V · Heintz-Buschart A · Laczny CC · May P · Wilmes P last · Nzabarushimana E first · Tang H last
Downloads
PRJNA297269.csv.gz (1.4 KB) · parquet (70.3 KB) — all 15 samples, every field with route and confidence · PRJNA297269_determinations.csv.gz (1.4 KB) — 75 evidence rows