PRJNA447983 SRP136711
Fecal metagenomes, Italian CRC case-control cohort
Whole-metagenome shotgun sequencing of two Italian fecal CRC cohorts
140 fecal samples from two Italian cohorts (Vercelli and Milan), including colorectal cancer, colorectal adenoma, and healthy control participants, studied in a case-control design. machine-written summary
140 samples · 140 runs · IT · Age unknown · 2018 · 3.76 Gbp / sample · cohort Metagenomic analysis of colorectal cancer datasets
Sources
✓Sequence archive 840✓Abstract / description 140○Full text✓Supplementary tables 559✓External resources 134–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 840 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 140 sample values (subject id) |
| ○ Full text | read; no usable statement or table · PMC12511565, PMC12818822, PMC13205780, PMC13387006, PMC6749105, PMC9533319 |
| ✓ Supplementary tables | 559 sample values (age, bmi, health condition, health condition detail, sex) |
| ✓ External resources | 134 sample values (age, bmi, health condition, health condition detail, sex) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
2 sampling locations · 1 country
Age
adult80
elderly59
unknown1
Condition
colorectal_cancer61
healthy_control52
colorectal_adenoma27
Sex
male91
female49
Country
IT140
Body site
primary140
Collected 2016–2017
Sequencing depth per sample · this project all projects
Community composition
Bacteroides 8.2%Prevotella 7.4%Phocaeicola 6.8%Alistipes 6.2%Faecalibacterium 5.7%Roseburia 3.6%Blautia_A 3.2%Bifidobacterium 2.9%Ruminococcoides 2.4%Gemmiger 2.3%Escherichia 1.8%Parabacteroides 1.6%not assigned to a genus 7.0%other genera 40.9%
Genera, mean relative abundance over 124 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 | 139 | 99% | ||||
| country | 140 | 100% | 140 | |||
| health_condition | 140 | 100% | 140 | |||
| subject_id | 140 | 100% | 140 | |||
| collection_date | 140 | 100% | 140 | |||
| detailed_location | 140 | 100% | ||||
| health_condition_detail | 140 | 100% | 140 | |||
| latitude | 140 | 100% | 140 | |||
| location_locality | 140 | 100% | 140 | |||
| location_region | 140 | 100% | 140 | |||
| longitude | 140 | 100% | 140 | |||
| sex | 140 | 100% | 140 | |||
| age_at_collection_days | 139 | 99% | 139 | |||
| bmi | 134 | 96% | 134 |
Papers (52)
- Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. 2019 PMID 30936548 PMC9533319 own_data
- Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples. 2019 PMID 31530647 PMC6749105 own_data
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches. 2026 PMID 41530917 PMC12818822 own_data
- Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. 2019 PMID 30936547 PMC7984229 unsure
- Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment. 2020 PMID 32393180 PMC7216530 unsure
47 more
- Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers. 2021 PMID 33430705 PMC7808391
- Microbiome as Mediator of Diet on Colorectal Cancer Risk: The Role of Vitamin D, Markers of Inflammation and Adipokines. 2021 PMID 33504116 PMC7911673
- 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
- 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
- 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
- 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
- A novel promising diagnosis model for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene biomarkers. 2022 PMID 36572910 PMC9791776
- Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases. 2022 PMID 36778050 PMC9903723
- 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
- Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer. 2023 PMID 37635357 PMC10464540
- 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
- Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. 2023 PMID 37905808 PMC10734426
- 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
- Establishing a novel inflammatory bowel disease prediction model based on gene markers identified from single nucleotide variants of the intestinal microbiota. 2022 PMID 38868717 PMC10989788
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. 2024 PMID 38884260 PMC11317153
- Is There an Interplay between Environmental Factors, Microbiota Imbalance, and Cancer Chemotherapy-Associated Intestinal Mucositis? 2024 PMID 39204125 PMC11357004
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655
- 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
- Metagenomics reveals an increased proportion of an <i>Escherichia coli</i>-dominated enterotype in elderly Chinese people. 2025 PMID 40436643 PMC12119184
- 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
- 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
- Megasphaera Elesdenii Dysregulates Colon Epithelial Homeostasis, Aggravates Colitis-Associated Tumorigenesis. 2025 PMID 40801433 PMC12591162
- 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
- Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification. 2025 PMID 41283667 PMC12710343
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome. 2025 PMID 41345980 PMC12781464
- 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
- Instance-based transfer learning enables cross-cohort early detection of colorectal cancer. 2026 PMID 42106361 PMC13381771
- Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data. 2026 PMID 42262136 PMC13387006
- 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
Details
Archive description
We used state-of-the-art whole-metagenome shotgun sequencing analysis methods to uniformly quantify taxonomic and functional abundance in fecal CRC metagenomes from 140 participants recruited in two new Italian cohorts.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “fecal CRC metagenomes from 140 participants”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08813920 | age_at_collection_days | 24106 | R2 | 0.85 | paper.supp.KGMI_A_2611544_SM3880.xlsx[Table S8!Host age] | 66 |
| SAMN08813981 | age_at_collection_days | 24837.0 | R2 | 0.75 | external.gmrepo source | host_age: 68.0 |
| SAMN08813920 | bmi | 21.1 | R2 | 0.85 | paper.supp.KGMI_A_2611544_SM3880.xlsx[Table S8!Host body mass index] | 21.09375 |
| SAMN08813981 | bmi | 30.0 | R2 | 0.75 | external.gmrepo source | BMI: 30.0 |
| SAMN08813920 | collection_date | 2016-01-11 | R1 | 0.90 | biosample.attribute:collection_date | 2016-01-11 |
| SAMN08813920 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy: Milan |
| SAMN08813920 | health_condition | healthy_control | R2 | 0.80 | paper.supp.KGMI_A_2611544_SM3880.xlsx[Table S8!Disease group] | Control |
| SAMN08813981 | health_condition | colorectal_adenoma | R2 | 0.75 | external.gmrepo source | phenotype: Adenomatous Polyps |
| SAMN08813920 | health_condition_detail | Control | R2 | 0.85 | paper.supp.KGMI_A_2611544_SM3880.xlsx[Table S8!Disease group] | Control |
| SAMN08813981 | health_condition_detail | Adenomatous Polyps | R2 | 0.75 | external.gmrepo source | phenotype: Adenomatous Polyps |
| SAMN08813920 | latitude | 45.4140 | R1 | 0.90 | biosample.attribute:lat_lon | 45.414028 N 9.208268 E |
| SAMN08813920 | location_locality | Milan | R1 | 0.85 | biosample.attribute:geo_loc_name | Italy: Milan |
| SAMN08813920 | location_region | Lombardy | R1 | 0.60 | biosample.attribute:lat_lon | 45.414028 N 9.208268 E |
| SAMN08813920 | longitude | 9.2083 | R1 | 0.90 | biosample.attribute:lat_lon | 45.414028 N 9.208268 E |
| SAMN08813920 | sex | female | R2 | 0.85 | paper.supp.KGMI_A_2611544_SM3880.xlsx[Table S8!Host sex] | Female |
| SAMN08813981 | sex | female | R2 | 0.75 | external.gmrepo source | sex: Female |
| SAMN08813920 | subject_id | SAMN08813920 | R4 | 0.60 | design.one_sample_per_subject:description | fecal CRC metagenomes from 140 participants recruited in two new Italian cohorts |
Sequencing
140 runs over 140 samples · mean 4.47 Gbp per run (median 3.76 Gbp, total 625.31 Gbp; 140 runs with a base count) · layout PAIRED 140 · platform ILLUMINA 140 · models Illumina HiSeq 2500 (140) · 89% of runs with a Sandpiper profile · first public 2018-08-15
Authors (91)
Thomas AM first · Manghi P · Asnicar F · Pasolli E · Armanini F · Zolfo M · Beghini F · Manara S · Karcher N · Pozzi C · Gandini S · Serrano D · Tarallo S · Francavilla A · Gallo G · Trompetto M · Ferrero G · Mizutani S · Shiroma H · Shiba S · Shibata T · Yachida S · Yamada T · Wirbel J · Schrotz-King P · Ulrich CM · Brenner H · Arumugam M · Bork P · Zeller G · Cordero F · Dias-Neto E · Setubal JC · Tett A · Pardini B · Rescigno M · Waldron L · Naccarati A · Segata N last · Wu Y first · Ji G · Han D · Zhang Y · Zhu X · Li H · Li M · Gao Y · Xie R · Xu M · Lu L · Deng Z · Wei Q · Qin H · Bi D 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 · Schroer HW first · Raygoza Garay JA · Christakis NA · Bosch DE last · Iacovacci J first · Cannon N · McCulloch JA · Rancati T · Trinchieri G last · Zhang Z first · Lu T · Dong B · Liu J · 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
Downloads
PRJNA447983.csv.gz (5.7 KB) · parquet (78.5 KB) — all 140 samples, every field with route and confidence · PRJNA447983_determinations.csv.gz (13.5 KB) — 1,673 evidence rows
Samples (140 · every field this project has values for · hover a cell for its source)
Loading the sample table…