Gut Microbiome and Frailty in Elderly Irish Adults
Cross-sectional shotgun metagenomic study of 214 fecal samples from elderly individuals in Ireland (ELDERMET cohort), examining gut microbiome markers associated with frailty and disease-related microbiome alterations with age. machine-written summary
214 samples · 214 runs · IE · Elderly · 2020 · 4.24 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,498 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10154212, PMC10829834, PMC10854441, PMC7065848 |
| ✓ Supplementary tables | 563 sample values (age, bmi, sex) |
| – 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
5 of 209 people sampled more than once (10 samples; median 2, up to 2 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 12 mo (time from age at collection). Schedule stated by the source: “Samples labeled by timepoint T0, T3, T6 per subject; n_catalog_samples(214) exceeds n_subj(209), indicating some subjects sampled at multiple timepoints.”.
Each row is one person (4 shown of 5); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 196 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 | 214 | 100% | ||||
| country | 214 | 100% | 214 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 214 | 100% | 214 | |||
| collection_date | 214 | 100% | 214 | |||
| detailed_location | 214 | 100% | ||||
| latitude | 214 | 100% | 214 | |||
| location_region | 214 | 100% | 214 | |||
| longitude | 214 | 100% | 214 | |||
| timepoint_label | 214 | 100% | 214 | |||
| age_at_collection_days | 188 | 88% | 188 | |||
| sex | 188 | 88% | 188 | |||
| bmi | 187 | 87% | 187 |
- Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model. 2023 PMID 38010168 PMC10854441 own_data
- A gut aging clock using microbiome multi-view profiles is associated with health and frail risk. 2024 PMID 38289284 PMC10829834 own_data
- Adjusting for age improves identification of gut microbiome alterations in multiple diseases. 2020 PMID 32159510 PMC7065848 unsure
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212 unsure
Archive description
In this study, we first show that disease-microbiome associations display specific age-centric trends. Ageing-associated microbiome alterations towards a disease-like configuration occur in colorectal cancer patients, thereby masking disease signatures. We identified a microbiome disease response shared across multiple diseases in elderly subjects that is distinct from that in young/middle-aged individuals, but also a novel set of taxa consistently gained in disease across all age groups. A subset of these taxa was associated with increased frailty in subjects from the ELDERMET cohort. The relevant taxa differentially encode specific functions that are known to have disease associations. The shotgun sequence data for the ELDERMET cohort is deposited here.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage study.title · “Elderly Irish Individuals”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6618415 | age_at_collection_days | 25933.0 | R2 | 0.85 | paper.supp.KGMI_A_2282796_SM5953.zip/Supplemental materials/Supplementary_HY_et_al.xlsx[Supplementary Table S6!Age] | Age: 71 |
| SAMEA6618415 | bmi | 31.40 | R2 | 0.85 | paper.supp.KGMI_A_2282796_SM5953.zip/Supplemental materials/Supplementary_HY_et_al.xlsx[Supplementary Table S6!BMI] | BMI: 31.4 |
| SAMEA6618415 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMEA6618415 | country | IE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Ireland |
| SAMEA6618415 | latitude | 51.8980 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.8979683 -8.4706097 |
| SAMEA6618415 | location_region | Munster | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.8979683 -8.4706097 |
| SAMEA6618415 | longitude | -8.4706 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.8979683 -8.4706097 |
| SAMEA6618415 | sex | male | R2 | 0.85 | paper.supp.KGMI_A_2282796_SM5953.zip/Supplemental materials/Supplementary_HY_et_al.xlsx[Supplementary Table S6!Sex] | Sex: male |
| SAMEA6618415 | subject_id | EM013 | R1 | 0.70 | sample.name_rule:alias | EM013_T0 |
| SAMEA6618415 | timepoint_label | T0 | R1 | 0.70 | sample.name_rule:alias | EM013_T0 |
Sequencing
214 runs over 214 samples · mean 4.15 Gbp per run (median 4.24 Gbp, total 888.76 Gbp; 214 runs with a base count) · layout PAIRED 214 · platform ILLUMINA 214 · models Illumina HiSeq 2000 (214) · 92% of runs with a Sandpiper profile · first public 2020-03-14
Authors (19)
Ghosh TS first · Das M · Jeffery IB · O'Toole PW last · Shanahan F · Ye H first · Hueston CM · Vlckova K · Golubeva AV · Hyland NP · Wang H first · Chen Y · Feng L · Lu S · Zhu J · Zhao J · Zhang H · Chen W · Lu W last
Downloads
PRJEB37017.csv.gz (7.3 KB) · parquet (80.3 KB) — all 214 samples, every field with route and confidence · PRJEB37017_determinations.csv.gz (16.9 KB) — 2,061 evidence rows