Microbiome & host genetics in cognitive disability, Japan
Whole-metagenome shotgun sequencing of 43 fecal samples from Japanese adults with varying cognitive disability. Study profiled host genotype and gut microbiota to investigate host-microbiome interactions in Alzheimer's disease. machine-written summary
43 samples · 43 runs · JP · Adult · 2021 · 21.28 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 215 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 43 sample values (subject id) · PMC11684920, PMC13069797, PMC8484692 |
| ✓ Supplementary tables | 215 sample values (age, bmi, health condition, health condition detail, 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 |
Genera, mean relative abundance over 39 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 | 43 | 100% | ||||
| country | 43 | 100% | 43 | |||
| health_condition | 43 | 100% | 43 | |||
| subject_id | 43 | 100% | 43 | |||
| age_at_collection_days | 43 | 100% | 43 | |||
| bmi | 43 | 100% | 43 | |||
| collection_date | 43 | 100% | 43 | |||
| detailed_location | 43 | 100% | ||||
| health_condition_detail | 43 | 100% | 43 | |||
| latitude | 43 | 100% | 43 | |||
| location_region | 43 | 100% | 43 | |||
| longitude | 43 | 100% | 43 | |||
| sex | 43 | 100% | 43 |
- Identification of <i>Faecalibacterium prausnitzii</i> strains for gut microbiome-based intervention in Alzheimer's-type dementia. 2021 PMID 34622235 PMC8484692 own_data
- Impacts of host genetics on gut microbiome composition in Alzheimer's disease. 2026 PMID 41782023 PMC13069797 own_data
- Secondary analysis reveals gut microbiota differences in patients with Parkinson's disease and/or cognitive impairment. 2024 PMID 39741952 PMC11684920 unsure
Archive description
Whole-metagenome shotgun sequencing of human feces
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 · “sequencing of human feces”
- body site study.description · “sequencing of human feces”
- 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 |
|---|---|---|---|---|---|---|
| SAMN16830156 | age_at_collection_days | 33238 | R2 | 0.80 | paper.supp.mmc2.xlsx[Table S3!Age (years)] | 91 |
| SAMN16830156 | bmi | 21.11 | R2 | 0.80 | paper.supp.mmc2.xlsx[Table S3!BMI (kg/m2)] | 21.11111111 |
| SAMN16830156 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN16830156 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan: Gumma |
| SAMN16830156 | health_condition | neurological_psychiatric | R2 | 0.80 | paper.supp.mmc2.xlsx[Table S3!Group (1: healthy, 2 MCI, 3: AD)] | 3 |
| SAMN16830156 | health_condition_detail | AD | R2 | 0.80 | paper.supp.mmc2.xlsx[Table S3!Group (1: healthy, 2 MCI, 3: AD)] | 3 |
| SAMN16830156 | latitude | 36.6210 | R1 | 0.90 | biosample.attribute:lat_lon | 36.621 N 138.59 E |
| SAMN16830156 | location_region | Gunma | R1 | 0.75 | biosample.attribute:geo_loc_name | Japan: Gumma |
| SAMN16830156 | longitude | 138.5900 | R1 | 0.90 | biosample.attribute:lat_lon | 36.621 N 138.59 E |
| SAMN16830156 | sex | male | R2 | 0.80 | paper.supp.mmc2.xlsx[Table S3!Gender] | M |
| SAMN16830156 | subject_id | SAMN16830156 | R3 | 0.75 | design.one_sample_per_subject:fulltext | We first performed our own cross-sectional study to identify potential MCI-preventive microbes. |
Sequencing
43 runs over 43 samples · mean 21.99 Gbp per run (median 21.28 Gbp, total 945.56 Gbp; 43 runs with a base count) · layout PAIRED 43 · platform ILLUMINA 43 · models Illumina HiSeq 2500 (43) · 91% of runs with a Sandpiper profile · first public 2021-09-15
Authors (54)
Ueda A first · Shinkai S · Shiroma H · Taniguchi Y · Tsuchida S · Kariya T · Kawahara T · Kobayashi Y · Kohda N · Ushida K · Kitamura A · Yamada T last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Shen X first · Leng B · Zhang S · Kwok LY · Zhao F · Zhao J · Sun Z · Zhang J last · Liu J first · Cao J · Jia L · Gan Z · Zhao X · Yang A · Lai S · Chen F · Yang YT · Zhao XM last
Downloads
PRJNA679346.csv.gz (2.4 KB) · parquet (72.6 KB) — all 43 samples, every field with route and confidence · PRJNA679346_determinations.csv.gz (4.7 KB) — 473 evidence rows