Gut microbiome in prediabetes and obesity, Japan
Cross-sectional study of 290 fecal samples from healthy, obese, and prediabetic Japanese adults, profiled by 16S rRNA amplicon and shotgun metagenomic sequencing to examine gut microbiota links to insulin resistance. machine-written summary
290 samples · 290 runs · JP · Adult · 2023 · 8.46 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,160 sample values (collection date, country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 580 sample values (location site, subject id) · PMC10499599 |
| ○ 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 |
Genera, mean relative abundance over 263 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 | 290 | 100% | ||||
| country | 290 | 100% | 290 | |||
| health_condition | 290 | 100% | 290 | |||
| subject_id | 290 | 100% | 290 | |||
| collection_date | 290 | 100% | 290 | |||
| detailed_location | 290 | 100% | ||||
| health_condition_detail | 290 | 100% | 290 | |||
| location_site | 290 | 100% | 290 |
- Gut microbial carbohydrate metabolism contributes to insulin resistance. 2023 PMID 37648852 PMC10499599 own_data
- Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis. 2026 PMID 42289444 PMC13526866 unsure
- Biome-specific genome catalogues reveal functional potential of shallow sequencing 2025 unsure
Archive description
Fecal samples of 306 healthy, obese, and prediabetic Japanese adults were collected. The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon pyrosequencing was carried out using Illumina MiSeq. Metagenome shotgun libraries (insert size of 500 bp) were prepared using the TruSeq Nano DNA kit (Illumina) and sequenced by the Illumina NovaSeq platform.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Fecal samples of 306 healthy, obese, and prediabetic”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “prediabetic Japanese adults were collected”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00291500 | collection_date | 2017-09-11 | R1 | 0.90 | biosample.attribute:collection_date | 2017-09-11 |
| SAMD00291500 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00291500 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: Fecal sample of normoglycemic lean group |
| SAMD00291500 | health_condition_detail | Fecal sample of normoglycemic lean group | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: Fecal sample of normoglycemic lean group |
| SAMD00291500 | location_site | University of Tokyo Hospital | R3 | 0.70 | paper.fulltext.methods | health check-ups at the University of Tokyo Hospital |
| SAMD00291500 | subject_id | SAMD00291500 | R3 | 0.70 | design.one_sample_per_subject:fulltext | faecal metagenomics data were available for 290 individuals |
Sequencing
290 runs over 290 samples · mean 8.70 Gbp per run (median 8.46 Gbp, total 2,523.47 Gbp; 290 runs with a base count) · layout PAIRED 290 · platform ILLUMINA 290 · models Illumina NovaSeq 6000 (290) · 91% of runs with a Sandpiper profile · first public 2023-04-06 – 2023-04-08
Authors (40)
Takeuchi T first · Kubota T · Nakanishi Y · Tsugawa H · Suda W · Kwon AT · Yazaki J · Ikeda K · Nemoto S · Mochizuki Y · Kitami T · Yugi K · Mizuno Y · Yamamichi N · Yamazaki T · Takamoto I · Kubota N · Kadowaki T · Arner E · Carninci P · Ohara O · Arita M · Hattori M · Koyasu S · Ohno H last · Masuoka H first · Miyatake T · Park J · Negishi H · Kurokawa R · Tsuchihashi H · Makino S · Escobar-Zepeda A first · Ruuskanen MO · Beracochea M · Lu J · Mongad D · Richardson L · Finn RD · Lahti L last
Downloads
PRJDB11444.csv.gz (8.5 KB) · parquet (82.4 KB) — all 290 samples, every field with route and confidence · PRJDB11444_determinations.csv.gz (11.4 KB) — 1,740 evidence rows