Gut metagenomes in elderly dementia patients, Massachusetts
79 gut metagenome samples from elderly patients with advanced dementia in long-term care facilities in Massachusetts, USA, examined in a case-control study of antimicrobial resistance gene density and pathobiont abundance. machine-written summary
79 samples · 79 runs · US · Age unknown · 2019 · 5.68 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 552 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 158 sample values (health condition detail, lifestyle detail) |
| ✓ Full text | 79 sample values (lifestyle) · PMC6777474, PMC7044522 |
| ○ 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
Residents with advanced dementia from 23 nursing homes (SPREAD); the home of each sample is not stated, so no per-sample setting rows.
Genera, mean relative abundance over 71 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 | 79 | 100% | ||||
| country | 79 | 100% | 79 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 79 | 100% | 79 | |||
| collection_date | 79 | 100% | 79 | |||
| detailed_location | 79 | 100% | ||||
| health_condition_detail | 79 | 100% | 79 | |||
| latitude | 79 | 100% | 79 | |||
| lifestyle | 79 | 100% | 79 | |||
| lifestyle_detail | 79 | 100% | 79 | |||
| location_region | 79 | 100% | 79 | |||
| longitude | 79 | 100% | 79 | |||
| timepoint_label | 78 | 99% | 78 |
- Fecal Microbiome Characteristics and the Resistome Associated With Acquisition of Multidrug-Resistant Organisms Among Elderly Subjects. 2019 PMID 31611867 PMC6777474 own_data
- Antimicrobial Resistance Gene Prevalence in a Population of Patients with Advanced Dementia Is Related to Specific Pathobionts. 2020 PMID 32106056 PMC7044522 own_data
Archive description
Study to determine microbial indices predicting acquisition of multidrug-resistant organisms
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 run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11391594 | collection_date | 2010-02-03 | R1 | 0.90 | biosample.attribute:collection_date | 2010-02-03 |
| SAMN11391594 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Massachusetts |
| SAMN11391594 | health_condition_detail | mixed_case_control: Elderly nursing home residents (MDRO acquirers vs non-acquirers) vs healthy young controls. | R4 | 0.40 | paper.abstract | 82 elderly subjects from 23 nursing homes and compare their resistome to |
| SAMN11391594 | latitude | 42.2400 | R1 | 0.90 | biosample.attribute:lat_lon | 42.24 N 71.22 W |
| SAMN11391594 | lifestyle | institutionalized | R3 | 0.70 | paper.fulltext.abstract | elderly population residing in nursing homes |
| SAMN11391594 | lifestyle_detail | Elderly nursing home residents | R4 | 0.50 | paper.abstract | elderly population residing in nursing homes |
| SAMN11391594 | location_region | Massachusetts | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Massachusetts |
| SAMN11391594 | longitude | -71.2200 | R1 | 0.90 | biosample.attribute:lat_lon | 42.24 N 71.22 W |
| SAMN11391594 | subject_id | S02_007 | R1 | 0.65 | sample.name_rule:alias | S02_007_3_6_R |
| SAMN11391594 | timepoint_label | month 3 | R1 | 0.70 | sample.name_rule:alias | S02_007_3_6_R |
Sequencing
79 runs over 79 samples · mean 5.88 Gbp per run (median 5.68 Gbp, total 464.23 Gbp; 79 runs with a base count) · layout PAIRED 79 · platform ILLUMINA 79 · models Illumina HiSeq 4000 (79) · 90% of runs with a Sandpiper profile · first public 2019-05-11 – 2019-06-30
Authors (8)
Araos R first · Battaglia T · Ugalde JA · Rojas-Herrera M · Blaser MJ · D'Agata EMC last · Rowan-Nash AD first · Belenky P last
Downloads
PRJNA531921.csv.gz (3.8 KB) · parquet (75.4 KB) — all 79 samples, every field with route and confidence · PRJNA531921_determinations.csv.gz (7.1 KB) — 789 evidence rows