Gut Microbiome in Elderly Advanced Dementia Patients, Boston
38 gut microbiome samples from elderly patients with advanced dementia in the Greater Boston Area, MA, USA, examining effects of the antimicrobial levofloxacin on pathogen abundance and antimicrobial resistance genes (intervention study). machine-written summary
38 samples · 38 runs · US · Adult · 2019 · 6.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 418 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
longitudinal
11 of 11 people sampled more than once (38 samples; median 4, up to 5 per person) · follow-up median 9 mo (max 12 mo) · median interval between samples 3 mo (time from collection dates).
Each row is one person (11 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 33 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 | 38 | 100% | ||||
| country | 38 | 100% | 38 | |||
| health_condition | 38 | 100% | 38 | |||
| subject_id | 38 | 100% | 38 | |||
| age_at_collection_days | 38 | 100% | 38 | |||
| antibiotic_exposure | 38 | 100% | 38 | |||
| collection_date | 38 | 100% | 38 | |||
| detailed_location | 38 | 100% | ||||
| health_condition_detail | 38 | 100% | 38 | |||
| location_locality | 38 | 100% | 38 | |||
| location_region | 38 | 100% | 38 | |||
| sex | 38 | 100% | 38 | |||
| timepoint_label | 38 | 100% | 38 |
- Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts 2019 own_data
Archive description
The issue of antimicrobial resistance continues to grow worldwide, and long-term care facilities are significant reservoirs of antimicrobial-resistant organisms, in part due to high frequency of antimicrobial use. Patients with advanced dementia are particularly vulnerable to multidrug-resistant organism acquisition and antimicrobial overuse, which has negative consequences for the gut microbiome and can contribute to the selection and propagation of antimicrobial resistance genes. In this study, we examined the impacts of the fluoroquinolone antimicrobial levofloxacin on the gut microbiome of advanced dementia patients and the correlation between abundance of pathogens and antimicrobial resistance genes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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 · “Gut Microbiome of Elderly”
- body site study.description · “consequences for the gut microbiome and can”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.title · “Microbiome of Elderly Adults with Advanced Dementia”
- life stage study.title · “Gut Microbiome of Elderly Adults with Advanced”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12837464 | age_at_collection_days | 34303.5 | R1 | 0.85 | sample.attr.host_age | 94 |
| SAMN12837464 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:chem_administration | Not Applicable |
| SAMN12837464 | collection_date | 2010-09-27 | R1 | 0.90 | biosample.attribute:collection_date | 2010-09-27 |
| SAMN12837464 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Greater Boston Area, MA |
| SAMN12837464 | health_condition | neurological_psychiatric | R1 | 0.90 | biosample_attr | Advanced Dementia (Alzheimer's) |
| SAMN12837464 | health_condition_detail | Advanced Dementia (Alzheimer's) | R1 | 0.90 | sample.attr.host_disease | Advanced Dementia (Alzheimer's) |
| SAMN12837464 | location_locality | Greater Boston Area | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Greater Boston Area, MA |
| SAMN12837464 | location_region | Massachusetts | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Greater Boston Area, MA |
| SAMN12837464 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN12837464 | subject_id | A | R1 | 0.85 | sample.attr.host_subject_id | A |
| SAMN12837479 | subject_id | F | R1 | 0.85 | biosample.attribute:host_subject_id | F |
| SAMN12837464 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:alias | A0_SM |
Sequencing
38 runs over 38 samples · mean 6.30 Gbp per run (median 6.43 Gbp, total 239.40 Gbp; 38 runs with a base count) · layout PAIRED 38 · platform ILLUMINA 38 · models Illumina HiSeq 4000 (38) · 87% of runs with a Sandpiper profile · first public 2019-09-27 – 2019-09-29
Authors (7)
Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last
Downloads
PRJNA573963.csv.gz (2.4 KB) · parquet (72.6 KB) — all 38 samples, every field with route and confidence · PRJNA573963_determinations.csv.gz (4.1 KB) — 418 evidence rows