Oral and stool metagenomes, long-term care residents, Japan
118 oral and stool samples from elderly long-term care facility residents in Japan, studying effects of antimicrobial treatment on the gut/oral microbiome and resistome, using a cross-sectional design. machine-written summary
118 samples · 118 runs · JP · Age unknown · 2023 · 11.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 396 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 236 sample values (lifestyle, lifestyle detail) · PMC10926694 |
| ✓ Supplementary tables | 274 sample values (age, 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 |
longitudinal — not resolvedcare home — not resolved
6 of 85 people sampled more than once (12 samples; median 2, up to 2 per person). Schedule stated by the source: “Most residents sampled once; 6 residents with fever gave a follow-up stool sample during (6-8 days) or 2-4 weeks after antimicrobial treatment” (time origin: intervention_start); stated follow-up 28 d.
Residents of six long-term care facilities (Japan); facility of each sample not given.
Genera, mean relative abundance over 85 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 | 118 | 100% | ||||
| country | 118 | 100% | 118 | |||
| health_condition | 63 | 53% | 63 | |||
| subject_id | 118 | 100% | 118 | |||
| collection_date | 118 | 100% | 118 | |||
| lifestyle | 118 | 100% | 118 | |||
| lifestyle_detail | 118 | 100% | 118 | |||
| age_at_collection_days | 74 | 63% | 74 | |||
| sex | 74 | 63% | 74 | |||
| health_condition_detail | 63 | 53% | 63 | |||
| timepoint_label | 42 | 36% | 42 |
- Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing. 2024 PMID 38376378 PMC10926694 own_data
Archive description
This project includes metagenome data from oral and stool samples, which were collected from Japanese long-term care facility residents in terms of antimicrobial treatment, and genome data of isolates from those samples.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human feces metagenome”
- body site study.title · “oral and stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00639423 | age_at_collection_days | 30681.0 | R2 | 0.80 | paper.supp.mgen-10-1180-s002.xlsx[stool!age] | age: 84 |
| SAMD00639371 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMD00639371 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00639423 | health_condition | neurological_psychiatric | R2 | 0.80 | paper.supp.mgen-10-1180-s002.xlsx[stool!dementina] | dementina: yes |
| SAMD00639423 | health_condition_detail | yes | R2 | 0.80 | paper.supp.mgen-10-1180-s002.xlsx[stool!dementina] | dementina: yes |
| SAMD00639371 | lifestyle | institutionalized | R3 | 0.70 | paper.fulltext.methods | recruited from six long-term care facilities |
| SAMD00639371 | lifestyle_detail | Long-term care facility residents | R3 | 0.70 | paper.fulltext.methods | long-term care facilities (specifically Geriatric Health Service Facilities) |
| SAMD00639423 | sex | male | R2 | 0.80 | paper.supp.mgen-10-1180-s002.xlsx[stool!gender] | gender: man |
| SAMD00639371 | subject_id | A10 | R1 | 0.70 | sample.name_rule:sample_name | OKA10 |
| SAMD00639468 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:sample_name | OKGU_10_1 |
Sequencing
118 runs over 118 samples · mean 12.19 Gbp per run (median 11.70 Gbp, total 1,438.03 Gbp; 118 runs with a base count) · layout PAIRED 118 · platform ILLUMINA 118 · models Illumina NovaSeq 6000 (118) · 94% of runs with a Sandpiper profile · first public 2023-09-17
Authors (16)
Kitamura N first · Kajihara T · Volpiano CG · Naung M · Méric G · Hirabayashi A · Yano H · Yamamoto M · Yoshida F · Kobayashi T · Yamanashi S · Kawamura T · Matsunaga N · Okochi J · Sugai M · Yahara K last
Downloads
PRJDB16443.csv.gz (4.5 KB) · parquet (75.9 KB) — all 118 samples, every field with route and confidence · PRJDB16443_determinations.csv.gz (7.1 KB) — 906 evidence rows