Longitudinal gut microbiome, nursing home elders, MA
489 stool samples from elderly nursing home residents in Massachusetts, USA, collected longitudinally to identify microbiome taxa associated with Alzheimer's Disease. machine-written summary
490 samples · 490 runs · US · Adult · 2020 · 0.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,444 sample values (collection date, country, location region, subject id, timepoint) |
| ✓ Abstract / description | 1,470 sample values (health condition detail, lifestyle, lifestyle detail) |
| ✓ Full text | 1 sample values (location region) · PMC12483529, PMC8007149 |
| ○ 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
longitudinalcare home — not resolved
125 of 174 people sampled more than once (437 samples; median 3, up to 12 per person) · follow-up median 2 mo (max 6 mo) · median interval between samples 30 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Monthly stool collection per resident for up to 5 months (observed day offsets include 0,2,5,8,11,14,15,16,17,20,23,25,30,45,60,90,120 days from enrollment).” (time origin: enrolment).
Each row is one person (36 shown of 125); dots are samples at days since that person's first sample.
Nursing-home elders from 5 facilities (paper); per-sample facility not deposited.
Genera, mean relative abundance over 364 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 | 490 | 100% | ||||
| country | 490 | 100% | 490 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 486 | 99% | 486 | |||
| detailed_location | 490 | 100% | ||||
| health_condition_detail | 490 | 100% | 490 | |||
| lifestyle | 490 | 100% | 490 | |||
| lifestyle_detail | 490 | 100% | 490 | |||
| location_region | 490 | 100% | 489 | 1 | ||
| timepoint_label | 490 | 100% | 490 | |||
| collection_date | 489 | 100% | 489 |
- The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome. 2021 PMID 33764826 PMC8007149 own_data
- ADAM-1: An AI Reasoning and Bioinformatics Model for Alzheimer's Disease Detection and Microbiome-Clinical Data Integration. 2025 PMID 41036149 PMC12483529 own_data
Archive description
Studies examining the intestinal microbiota of Alzheimer's Disease (AD) patients revealed that their microbiome differs from subjects without dementia. In this work, 108 nursing home elders were prospectively enrolled and followed for up to 5 months collecting longitudinal stool samples. Samples were subjected to metagenomic sequencing for identification of taxa that act as major predictors of AD.
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.description · “Studies examining the intestinal microbiota of Alzheimer's”
- body site external_curation.infant_catalog · “body_site_call stool”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “this work, 108 nursing home elders were prospectively”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11269715 | collection_date | 2016-07-01/2018-07-31 | R1 | 0.90 | biosample.attribute:collection_date | 2016-07-01/2018-07-31 |
| SAMN11269715 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Massachusetts |
| SAMN11269715 | health_condition_detail | mixed_case_control: Alzheimer's Disease patients vs subjects without dementia | R4 | 0.50 | study.description | microbiome differs from subjects without dementia |
| SAMN11269715 | lifestyle | institutionalized | R4 | 0.40 | ena.study_description | 108 nursing home elders were prospectively enrolled |
| SAMN11269715 | lifestyle_detail | nursing home elders | R4 | 0.40 | ena.study_description | 108 nursing home elders were prospectively enrolled |
| SAMN11269715 | location_region | Massachusetts | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Massachusetts |
| SAMN11269758 | location_region | Massachusetts | R3 | 0.70 | paper.fulltext.methods | five nursing home sites in central Massachusetts |
| SAMN11269715 | subject_id | CH1017 | R1 | 0.70 | sample.name_rule:title | subject_CH1017_specimen_1_day_0 |
| SAMN11269715 | timepoint_label | CH1017_day_0 | R1 | 0.85 | sample.attr.day_of_collection | CH1017_day_0 |
| SAMN11269758 | timepoint_label | day 0 | R1 | 0.85 | biosample.attribute:day_of_collection | CH1007_day_0 |
Sequencing
490 runs over 490 samples · mean 0.53 Gbp per run (median 0.38 Gbp, total 258.41 Gbp; 490 runs with a base count) · layout PAIRED 490 · platform ILLUMINA 490 · models NextSeq 500 (490) · 74% of runs with a Sandpiper profile · first public 2020-04-14 – 2024-02-25
Authors (13)
Haran JP first · Ward DV · Bhattarai SK · Loew E · Dutta P · Higgins A · McCormick BA · Bucci V last · Huang Z first · Kaur Sekhon V · Sadeghian R · Vaida ML · Jo C
Downloads
PRJNA529586.csv.gz (14.4 KB) · parquet (89.9 KB) — all 490 samples, every field with route and confidence · PRJNA529586_determinations.csv.gz (28.9 KB) — 3,915 evidence rows