PRJEB10878 ERP012177
Fecal metagenomes, CRC case-control cohort, China
Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer
128 fecal samples from China, including colorectal cancer patients, healthy controls, and type 2 diabetes samples, in a case-control metagenome-wide association study design. machine-written summary
128 samples · 128 runs · CN · Adult · 2015 · 5.59 Gbp / sample · cohort Contributions of Human-Associated Archaeal Metabol
Sources
✓Sequence archive 495✓Abstract / description 128○Full text○Supplementary tables✓External resources 511–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 495 sample values (collection date, country, health condition, health condition detail) |
| ✓ Abstract / description | 128 sample values (subject id) |
| ○ Full text | read; no usable statement or table · PMC10059959, PMC10154212, PMC10334131, PMC10338424, PMC10436198, PMC10556866, PMC10602384, PMC10673094, PMC10770074, PMC10897996, PMC11005914, PMC11009399, PMC11036815, PMC11229495, PMC11317153, PMC11334437, PMC11357004, PMC11402190, PMC11402979, PMC11418011, PMC11464690, PMC11510655, PMC11704624, PMC11980382, PMC11995172, PMC12133679, PMC12175378, PMC12274573, PMC12283368, PMC12326762, PMC12365777, PMC12449802, PMC12504321, PMC12511565, PMC12639245, PMC12683948, PMC12781464, PMC12844167, PMC12940152, PMC13035836, PMC13039525, PMC13205780, PMC13281578, PMC13377033, PMC13381771, PMC13402817, PMC13434703, PMC13561539, PMC6670193, PMC7157763, PMC7216530, PMC7228756, PMC7524397, PMC7962608, PMC7984229, PMC8096432, PMC8262883, PMC8269207, PMC8465708, PMC8511818, PMC8693921, PMC8715872, PMC8748837, PMC8801753, PMC8813618, PMC8853548, PMC9016944, PMC9040671, PMC9045267, PMC9096808, PMC9426597, PMC9454621, PMC9663839, PMC9665866, PMC9784093, PMC9791776, PMC9795735, PMC9975273 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 511 sample values (age, antibiotic exposure, bmi, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
1 country
Age
adult80
elderly48
Condition
colorectal_cancer74
healthy_control37
Sex
male81
female47
Country
CN128
Body site
primary128
Sequencing depth per sample · this project all projects
! Self-contradictory metadata
health condition: sequence archive and curatedMetagenomicData disagree for 17 samples (e.g. colorectal_cancer vs healthy_control) — withheld.
The sources disagree on 17 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 (17)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA3541487 | health condition | colorectal_cancer (sequence archive) | healthy_control (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541517 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541522 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541527 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541528 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541530 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541531 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541532 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541537 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541540 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541545 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541548 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541550 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541551 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541554 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541556 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA3541557 | health condition | healthy_control (sequence archive) | type2_diabetes (curatedMetagenomicData) | withheld: neither value published |
Community composition
Bacteroides 10.1%Phocaeicola 7.7%Faecalibacterium 4.7%Prevotella 4.5%Roseburia 3.8%Ruminococcoides 3.3%Escherichia 3.2%Fimenecus 2.4%Lachnospira 2.4%Bifidobacterium 2.3%Mediterraneibacter 2.1%Alistipes 2.0%not assigned to a genus 5.6%other genera 46.0%
Genera, mean relative abundance over 120 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 128 | 100% | ||||
| country | 128 | 100% | 128 | |||
| health_condition | 111 | 87% | 111 | |||
| subject_id | 128 | 100% | 128 | |||
| age_at_collection_days | 128 | 100% | 128 | |||
| antibiotic_exposure | 128 | 100% | 128 | |||
| collection_date | 128 | 100% | 128 | |||
| health_condition_detail | 128 | 100% | 128 | |||
| sex | 128 | 100% | 128 | |||
| bmi | 127 | 99% | 127 |
Papers (79)
- Bioinorganic hybrid bacteriophage for modulation of intestinal microbiota to remodel tumor-immune microenvironment against colorectal cancer. 2020 PMID 32440552 PMC7228756 own_data
- VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes. 2024 PMID 38965579 PMC11229495 own_data
- Microbial riboflavin inhibits ceramide synthase 3 to lower ceramide (d18:1/26:0) and delay colorectal cancer progression. 2025 PMID 40609532 PMC12365777 own_data
- MeTAline: enabling reproducible and scalable metagenomic analyses. 2025 PMID 41278541 PMC12639245 own_data
- Decoding the human gut bacterial plasmids in colorectal cancer. 2026 PMID 42141123 PMC13434703 own_data
74 more
- Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. 2019 PMID 30936547 PMC7984229
- Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease. 2019 PMID 31370880 PMC6670193
- Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families. 2020 PMID 31971861 PMC7524397
- Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. 2020 PMID 32265336 PMC7157763
- Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment. 2020 PMID 32393180 PMC7216530
- Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer. 2021 PMID 33738265 PMC7962608
- Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. 2021 PMID 33944776 PMC8096432
- Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models. 2021 PMID 33947803 PMC8269207
- Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. 2021 PMID 34061597 PMC8262883
- The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. 2021 PMID 34563136 PMC8465708
- Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. 2021 PMID 34659174 PMC8511818
- Expanding the Colorectal Cancer Biomarkers Based on the Human Gut Phageome. 2021 PMID 34935421 PMC8693921
- Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer. 2021 PMID 34975790 PMC8715872
- Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer. 2022 PMID 35013454 PMC8748837
- Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. 2022 PMID 35087227 PMC8813618
- Evaluating supervised and unsupervised background noise correction in human gut microbiome data. 2022 PMID 35130266 PMC8853548
- Increasing prediction performance of colorectal cancer disease status using random forests classification based on metagenomic shotgun sequencing data. 2022 PMID 35155839 PMC8801753
- Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis. 2022 PMID 35225671 PMC9045267
- Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. 2022 PMID 35240043 PMC9096808
- Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer. 2022 PMID 35440042 PMC9016944
- More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome. 2022 PMID 35493727 PMC9040671
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes. 2022 PMID 36077748 PMC9454621
- Integrating phylogenetic and functional data in microbiome studies. 2022 PMID 36179077 PMC9665866
- 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
- Alternation of the gut microbiota in metabolically healthy obesity: An integrated multiomics analysis. 2022 PMID 36389176 PMC9663839
- 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
- A novel promising diagnosis model for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene biomarkers. 2022 PMID 36572910 PMC9791776
- Using whole-genome sequencing (WGS) to plot colorectal cancer-related gut microbiota in a population with varied geography. 2022 PMID 36578080 PMC9795735
- Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype. 2023 PMID 36706753 PMC9975273
- 2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo. 2023 PMID 36984891 PMC10059959
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach. 2023 PMID 37457869 PMC10338424
- Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer. 2023 PMID 37601681 PMC10436198
- Machine learning approaches in microbiome research: challenges and best practices. 2023 PMID 37808286 PMC10556866
- Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies. 2023 PMID 37844077 PMC10602384
- The Archaeome's Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures. 2023 PMID 38004753 PMC10673094
- Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis. 2024 PMID 38182885 PMC10770074
- Identification of enterotype and its predictive value for patients with colorectal cancer. 2024 PMID 38414077 PMC10897996
- <i>Anaerostipes hadrus</i>, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil. 2024 PMID 38470044 PMC11036815
- Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis. 2024 PMID 38601936 PMC11005914
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. 2024 PMID 38884260 PMC11317153
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. 2024 PMID 39078158 PMC11334437
- The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri. 2024 PMID 39122003 PMC11418011
- Is There an Interplay between Environmental Factors, Microbiota Imbalance, and Cancer Chemotherapy-Associated Intestinal Mucositis? 2024 PMID 39204125 PMC11357004
- Gut bacterial type III secretion systems aggravate colitis in mice and serve as biomarkers of Crohn's disease. 2024 PMID 39216231 PMC11402190
- An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. 2024 PMID 39278950 PMC11402979
- 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
- RFW captures species-level metagenomic functions by integrating genome annotation information. 2024 PMID 39662474 PMC11704624
- The physical biogeography of <i>Fusobacterium nucleatum</i> in health and disease. 2025 PMID 40062772 PMC11980382
- Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects. 2025 PMID 40236771 PMC11995172
- Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer. 2025 PMID 40461820 PMC12283368
- Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology. 2025 PMID 40462511 PMC12133679
- Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer. 2025 PMID 40528214 PMC12175378
- Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation. 2025 PMID 40681522 PMC12274573
- Metabolic cross-feeding of a dietary antioxidant enhances anaerobic energy metabolism by human gut bacteria. 2025 PMID 40763732 PMC12683948
- Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer. 2025 PMID 40770383 PMC12326762
- Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach. 2025 PMID 40973961 PMC12449802
- Fusobacterium lineage profiling facilitates the clarification of the associations between non-nucleatum Fusobacterium and colorectal cancer. 2025 PMID 41068096 PMC12511565
- Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models. 2025 PMID 41070134 PMC12504321
- 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
- 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
- Landscape of flavonoid metabolism in human gut microbiome and its association with health and disease. 2025 PMID 41909884 PMC12940152
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data. 2026 PMID 42103726 PMC13377033
- Instance-based transfer learning enables cross-cohort early detection of colorectal cancer. 2026 PMID 42106361 PMC13381771
- Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis. 2026 PMID 42271362 PMC13281578
- Obesity-driven microbial GABA depletion promotes metabolic rewiring and colorectal cancer progression. 2026 PMID 42503520 PMC13402817
- Fedflow: cloud orchestration for federated learning with the FeatureCloud platform. 2026 PMID 42725323 PMC13561539
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Details
Archive description
We performed a metagenome-wide association study on fecal samples from 74 CRC patients and 54 controls from China and validated the results in 16 patients and 24 controls from Denmark. We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate the diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls.
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 · “Metagenomic analysis of fecal microbiome as a”
- body site study.description · “association study on fecal samples from 74”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA3541469 | age_at_collection_days | 23376.0 | R2 | 0.75 | external.cmd source | age: 64; age_unit: Year; age_group: Adult |
| SAMEA3541469 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA3541469 | bmi | 23.1 | R2 | 0.75 | external.cmd source | bmi: 23.1 |
| SAMEA3541469 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMEA3541469 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA3541469 | health_condition | colorectal_cancer | R1 | 0.85 | biosample.attribute:config | case |
| SAMEA3541469 | health_condition_detail | case | R1 | 0.90 | sample.attr.config | case |
| SAMEA3541469 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMEA3541469 | subject_id | SAMEA3541469 | R4 | 0.60 | design.one_sample_per_subject:abstract | faecal samples from 74 patients with CRC and 54 controls from China |
Sequencing
128 runs over 128 samples · mean 5.40 Gbp per run (median 5.59 Gbp, total 691.59 Gbp; 128 runs with a base count) · layout PAIRED 128 · platform ILLUMINA 128 · models Illumina HiSeq 2000 (128) · 94% of runs with a Sandpiper profile · first public 2015-10-01
Authors (59)
Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · Wang HW first · Li W · Ma QJ · Zhang HY · Quan Y · Zhu Q last · Goulet L first · Plaza Oñate F · Famechon A · Quinquis B · Belda E · Prifti E · Le Chatelier E · Gautreau G last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE 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 · Weilguny L first · Probul N · Ren Y · Pons N · Baumbach J · Almeida M last
Downloads
PRJEB10878.csv.gz (5.0 KB) · parquet (76.6 KB) — all 128 samples, every field with route and confidence · PRJEB10878_determinations.csv.gz (12.1 KB) — 1,134 evidence rows
Samples (128 · every field this project has values for · hover a cell for its source)
Loading the sample table…