Gut metagenome in HTLV-1 carriers and ATL patients, Japan
Cross-sectional study of 25 fecal samples from Japanese patients at Miyazaki University Hospital and Imamura General Hospital, comparing healthy individuals, HTLV-1 carriers, and adult T-cell leukemia (ATL) patients; ages spanned adult and elderly categories. machine-written summary
25 samples · 25 runs · JP · Age unknown · 2024 · 20.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 175 sample values (age, collection date, country, health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11619966 |
| – 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 |
Genera, mean relative abundance over 23 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 | 25 | 100% | ||||
| country | 25 | 100% | 25 | |||
| health_condition | 25 | 100% | 25 | |||
| subject_id | 25 | 100% | 25 | |||
| age_at_collection_days | 25 | 100% | 25 | |||
| collection_date | 25 | 100% | 25 | |||
| health_condition_detail | 25 | 100% | 25 | |||
| sex | 25 | 100% | 25 |
- Succinic semialdehyde derived from the gut microbiota can promote the proliferation of adult T-cell leukemia/lymphoma cells. 2024 PMID 39640675 PMC11619966 own_data
Archive description
Total microbial community DNA was isolated from the fecal samples of Japanese patients who were confirmed infected with HTLV-1 at Miyazaki University Hospital and Imamura General Hospital in Japan. The study population contains health, HTLV-1 carrier, and ATL.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “fecal samples of Japanese patients”
- body site study.description · “fecal samples”
- life stage sample.attr.age · “64 (n=14/25)”
- life stage sample.attr.age · “31 (n=11/25)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00639726 | age_at_collection_days | 13879.5 | R1 | 0.70 | sample.attr.age | 38 |
| SAMD00639726 | collection_date | 2016-03-01 | R1 | 0.90 | biosample.attribute:collection_date | 2016-03-01 |
| SAMD00639726 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00639726 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | gut microbiomes isolated from feces of Healthy control subject wgs_M01 |
| SAMD00639726 | health_condition_detail | Healthy | R1 | 0.70 | sample.name_rule:title | gut microbiomes isolated from feces of Healthy control subject wgs_M01 |
| SAMD00639726 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMD00639726 | subject_id | M01 | R1 | 0.85 | sample.attr.host_subject_id | M01 |
Sequencing
25 runs over 25 samples · mean 20.67 Gbp per run (median 20.18 Gbp, total 516.64 Gbp; 25 runs with a base count) · layout PAIRED 25 · platform ILLUMINA 25 · models Illumina NovaSeq 6000 (25) · 92% of runs with a Sandpiper profile · first public 2024-08-04
Authors (0)
No author record.
Downloads
PRJDB16532.csv.gz (1.8 KB) · parquet (70.8 KB) — all 25 samples, every field with route and confidence · PRJDB16532_determinations.csv.gz (2.2 KB) — 175 evidence rows