Gut metagenomes in Japanese colorectal cancer case-control study
645 fecal metagenome samples from Japanese adults and elderly patients undergoing colonoscopy, comparing healthy controls, colorectal adenoma, colorectal cancer, and other cancer cases in a case-control design. machine-written summary
645 samples · 645 runs · JP · Adult · 2019 · 6.49 Gbp / sample · cohort <i>Fusobacterium</i> species are disti
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,990 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region) |
| ✓ Abstract / description | 768 sample values (health condition detail, location site) |
| ○ Full text | read; no usable statement or table · PMC10920697, PMC11237946, PMC13378470, PMC13553305, PMC8011136, PMC9465070 |
| ✓ Supplementary tables | 665 sample values (age, bmi, health condition, health condition detail, sex) |
| ✓ External resources | 1,930 sample values (age, bmi, health condition, health condition detail, sex) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
age: supplementary table and Meta2DB disagree for 1 sample (e.g. 31777 vs 21915.0) — withheld; sex differs between samples of the same subject id (1 subjects, 2 samples) — sex withheld; subject ids shared by samples of both sexes (1 ids, 2 samples) — ids withheld.
The sources disagree on 3 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (5)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMD00114949 | age | 31777 (supplementary table) | 21915.0 (Meta2DB) | withheld: neither value published |
| SAMD00114782 | sex | female (sequence archive) | subject 10303: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMD00115085 | sex | male (Meta2DB) | subject 10303: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMD00114782 | subject id | 10303 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMD00115085 | subject id | 10303 | male (Meta2DB) | subject id withheld (samples of both sexes share it) |
longitudinal
27 of 616 people sampled more than once (54 samples; median 2, up to 2 per person) · follow-up median 5.0 y (max 5.0 y) · median interval between samples 5.0 y (time from age at collection).
Each row is one person (1 shown of 27); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 591 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 | 645 | 100% | ||||
| country | 645 | 100% | 645 | |||
| health_condition | 617 | 96% | 80 | 537 | ||
| subject_id | 643 | 100% | 643 | |||
| collection_date | 645 | 100% | 645 | |||
| detailed_location | 645 | 100% | ||||
| health_condition_detail | 645 | 100% | 80 | 442 | 123 | |
| latitude | 645 | 100% | 645 | |||
| location_site | 645 | 100% | 645 | |||
| longitude | 645 | 100% | 645 | |||
| sex | 623 | 97% | 79 | 544 | ||
| age_at_collection_days | 616 | 96% | 80 | 536 | ||
| bmi | 616 | 96% | 80 | 536 | ||
| location_region | 368 | 57% | 368 |
- Bacterial community structure alterations within the colorectal cancer gut microbiome. 2021 PMID 33789570 PMC8011136 own_data
- Clinical strains isolated from early-stage colorectal cancer patients promote tumorigenesis. 2026 PMID 42491728 PMC13378470 own_data
- Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer. 2026 PMID 42576026 PMC13553305 own_data
- Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment. 2020 PMID 32393180 PMC7216530 unsure
- Bacterial associations in the healthy human gut microbiome across populations. 2021 PMID 33531651 PMC7854710 unsure
36 more
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- Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer. 2021 PMID 34975790 PMC8715872
- Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. 2022 PMID 35087227 PMC8813618
- Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex. 2022 PMID 35536747 PMC9465070
- Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment. 2023 PMID 36198381 PMC10334131
- Metagenomic analysis of the interaction between the gut microbiota and colorectal cancer: a paired-sample study based on the GMrepo database. 2022 PMID 36564826 PMC9784093
- Using whole-genome sequencing (WGS) to plot colorectal cancer-related gut microbiota in a population with varied geography. 2022 PMID 36578080 PMC9795735
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- Metagenomic analysis reveals gut plasmids as diagnosis markers for colorectal cancer. 2023 PMID 37283932 PMC10239823
- Machine learning approaches in microbiome research: challenges and best practices. 2023 PMID 37808286 PMC10556866
- The Archaeome's Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures. 2023 PMID 38004753 PMC10673094
- Identification of enterotype and its predictive value for patients with colorectal cancer. 2024 PMID 38414077 PMC10897996
- Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia. 2024 PMID 38454103 PMC10920697
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. 2024 PMID 38565143 PMC11081829
- <i>Fusobacterium</i> species are distinctly associated with patients with Lynch syndrome colorectal cancer. 2024 PMID 38993678 PMC11237946
- Is There an Interplay between Environmental Factors, Microbiota Imbalance, and Cancer Chemotherapy-Associated Intestinal Mucositis? 2024 PMID 39204125 PMC11357004
- Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change. 2024 PMID 39384807 PMC11464690
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655
- Metagenomics reveals an increased proportion of an <i>Escherichia coli</i>-dominated enterotype in elderly Chinese people. 2025 PMID 40436643 PMC12119184
- Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer. 2025 PMID 40528214 PMC12175378
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848
- Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer. 2025 PMID 40770383 PMC12326762
- Systematically investigating and identifying bacteriocins in the human gut microbiome. 2025 PMID 40902606 PMC12648112
- Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer. 2025 PMID 41068096 PMC12511565
- Long-read metagenomics reveals phage dynamics in the human gut microbiome. 2026 PMID 41299176 PMC12823448
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome. 2025 PMID 41345980 PMC12781464
- Co-Metabolic Network Reveals the Metabolic Mechanism of Host-Microbiota Interplay in Colorectal Cancer. 2026 PMID 41590671 PMC12844167
- Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis. 2026 PMID 41654659 PMC12992544
- Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. 2026 PMID 41720792 PMC13035836
- The landscape of tissue-resident microbiota across normal, polyp, and colorectal cancer tissues. 2026 PMID 41730886 PMC13039525
- Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome. 2026 PMID 41869887 PMC13205780
- A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production. 2026 PMID 42039832 PMC13106387
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data. 2026 PMID 42103726 PMC13377033
- Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis. 2026 PMID 42271362 PMC13281578
- Pangenome analysis reveals both niche-specific "specialists" and microbial "side hustlers" in colorectal cancer microbiomes. 2026 PMID 42740607 PMC13580483
Archive description
Total microbial community DNA was isolated from the fecal samples of Japanese patients who underwent colonoscopy at National Cancer Research Center. The study population contains health, early and advanced cancer stages.
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 · “data from human fecal samples”
- body site study.description · “isolated from the fecal samples of Japanese”
- 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 |
|---|---|---|---|---|---|---|
| SAMD00114722 | age_at_collection_days | 23376.0 | R1 | 0.70 | sample.attr.age | 64 |
| SAMD00114718 | age_at_collection_days | 24837.0 | R2 | 0.70 | external.meta2db source | host_age: 68 |
| SAMD00114728 | age_at_collection_days | 16436 | R2 | 0.80 | paper.supp.41588_2026_2692_MOESM4_ESM.xlsx[Supplementary _Table_1!Age] | 45 |
| SAMD00114722 | bmi | 22.46 | R1 | 0.90 | sample.attr.body_mass_index | 22.4600343506408 |
| SAMD00114718 | bmi | 21.3839 | R2 | 0.70 | external.meta2db source | host_body_mass_index: 21.383942 kilogram per meter squared |
| SAMD00114728 | bmi | 20.62 | R2 | 0.80 | paper.supp.41588_2026_2692_MOESM4_ESM.xlsx[Supplementary _Table_1!Body mass index] | 20.61925365 |
| SAMD00114718 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMD00114718 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00114722 | health_condition | colorectal_cancer | R1 | 0.70 | biosample_attr | CRC (Stage III/IV) |
| SAMD00114718 | health_condition | healthy_control | R2 | 0.70 | external.meta2db source | health_disease_stat: control |
| SAMD00114736 | health_condition | healthy_control | R2 | 0.80 | paper.supp.41588_2026_2692_MOESM4_ESM.xlsx[Supplementary _Table_2!Group] | Healthy |
| SAMD00114722 | health_condition_detail | CRC (Stage III/IV) | R1 | 0.90 | sample.attr.host_disease_stat | CRC (Stage III/IV) |
| SAMD00114723 | health_condition_detail | colorectal cancer | R2 | 0.70 | external.meta2db source | colorectal cancer |
| SAMD00114736 | health_condition_detail | Healthy | R2 | 0.80 | paper.supp.41588_2026_2692_MOESM4_ESM.xlsx[Supplementary _Table_2!Group] | Healthy |
| SAMD00114718 | health_condition_detail | mixed_case_control: healthy controls vs early-stage and advanced colorectal cancer patients | R4 | 0.50 | study.description | health, early and advanced cancer stages |
| SAMD00114718 | latitude | 35.6600 | R1 | 0.90 | biosample.attribute:lat_lon | 35.66 N 139.76 E |
| SAMD00114719 | location_region | Tokyo | R1 | 0.60 | biosample.attribute:lat_lon | 35.66 N 139.77 E |
| SAMD00114718 | location_site | National Cancer Research Center | R4 | 0.45 | ena.study_description | colonoscopy at National Cancer Research Center |
| SAMD00114718 | longitude | 139.7600 | R1 | 0.90 | biosample.attribute:lat_lon | 35.66 N 139.76 E |
| SAMD00114722 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMD00114718 | sex | male | R2 | 0.70 | external.meta2db source | host_sex: male |
| SAMD00114728 | sex | male | R2 | 0.80 | paper.supp.41588_2026_2692_MOESM4_ESM.xlsx[Supplementary _Table_1!Sex] | Male |
| SAMD00114718 | subject_id | 10219 | R1 | 0.70 | sample.name_rule:title | human feces_10219 |
Sequencing
645 runs over 645 samples · mean 6.54 Gbp per run (median 6.49 Gbp, total 4,218.80 Gbp; 645 runs with a base count) · layout PAIRED 645 · platform ILLUMINA 645 · models Illumina HiSeq 2500 (645) · 92% of runs with a Sandpiper profile · first public 2019-02-02 – 2019-05-30
Authors (103)
Orihara K first · Yahagi K · Watanabe Y · Sasai T · Hara T · Tsukuda N · Oki K · Fujimoto J · Matsuki T last · Ormaasen I first · Rudi K · Diep DB · Snipen L 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 · Nooij S first · Plomp N · Sanders IMJG · Schout L · van der Meulen AE · Terveer EM · Norman JM · Karcher N · Larralde MF · Vossen RHAM · Kloet SL · Faber KN · Harmsen HJM · Zeller GF · Kuijper EJ · Smits WK · Ducarmon QR last · Damgaard F first · Jespersen MG · Møller JK · Coia JE · Dessau RB · Sydenham TV · Strube ML · Møller-Jensen J · Justesen US last · Wang Z first · Guo S · Li J · Huang Q · Ning J · Xia B · Lv X · Liu X · Gao Z · Liu L · Song M · Wang J last · Goulet L first · Plaza Oñate F · Famechon A · Quinquis B · Belda E · Prifti E · Le Chatelier E · Gautreau G last · Zhang Z first · Lu T · Dong B · Liu J · Zhang Y · Li S · Liu H · Li X · Guan T · Guo H · Yan Q · Lei Z · Yu X · Wang L · Kang J · Li L · Zhao D last · Suzuki D first · Yang J · Obana N · Yachida S · Shiba S · Mizutani S · Takamaru H · Saito Y · Fukuda S · Yamada T last
Downloads
PRJDB4176.csv.gz (25.7 KB) · parquet (108.2 KB) — all 645 samples, every field with route and confidence · PRJDB4176_determinations.csv.gz (88.6 KB) — 7,353 evidence rows