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PRJNA429097 SRP128485

Gut microbiota in Chinese CRC, Chongqing, case-control

Microbiota Research on Chinses Colorectal Cancer

194 fecal samples from Chongqing, China, comparing colorectal cancer patients (99) and healthy controls (95), ages mostly adult, in a case-control study of gut microbiota. machine-written summary

194 samples · 194 runs · CN · Age unknown · 2019 · 5.77 Gbp / sample

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Sources
✓Sequence archive 582○Abstract / description○Full text○Supplementary tables✓External resources 970–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive582 sample values (collection date, country, location locality)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC10556866, PMC10770074, PMC11317153, PMC11510655, PMC12283368, PMC13561539, PMC7524397
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources970 sample values (age, antibiotic exposure, bmi, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3), GMrepo v3
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 country
Age
adult167
elderly20
unknown7
Condition
colorectal_cancer99
Sex
male117
female76
Country
CN194
Body site
primary194
Collected 2015–2016
2015: 7 samples2016: 187 samples20152016
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 194 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 5.77 Gbp per sample0130Gbp
! Self-contradictory metadata

health condition: curatedMetagenomicData and GMrepo disagree for 95 samples (e.g. healthy_control vs colorectal_cancer) — withheld.

The sources disagree on 95 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 (40 of 95)
samplefieldvalueother valuehandling
SAMN08335033health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335034health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335035health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335036health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335037health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335038health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335039health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335040health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335041health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335042health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335043health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335044health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335045health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335046health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335047health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335048health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335049health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335050health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335051health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335052health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335053health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335054health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335055health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335056health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335057health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335058health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335059health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335060health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335061health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335062health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335063health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335064health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335065health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335066health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335067health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335068health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335069health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335070health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335071health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
SAMN08335072health conditionhealthy_control (curatedMetagenomicData)colorectal_cancer (GMrepo)withheld: neither value published
Community composition
Phocaeicola 18.4%Bacteroides 15.6%Prevotella 15.1%Faecalibacterium 3.9%Roseburia 3.9%Alistipes 3.1%Lachnospira 2.2%Parabacteroides 1.9%Mediterraneibacter 1.5%Blautia_A 1.2%Escherichia 1.1%Ruminococcoides 1.0%not assigned to a genus 3.7%other genera 27.4%

Genera, mean relative abundance over 171 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category187 96%
country194 100%194
health_condition99 51%99
subject_id0 0%
collection_date194 100%194
detailed_location194 100%
health_condition_detail194 100%194
location_locality194 100%194
age_at_collection_days193 99%193
bmi193 99%193
sex193 99%193
antibiotic_exposure98 51%98
Papers (7)
  • Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families. 2020 PMID 31971861 PMC7524397 unsure
  • Machine learning approaches in microbiome research: challenges and best practices. 2023 PMID 37808286 PMC10556866 unsure
  • Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis. 2024 PMID 38182885 PMC10770074 unsure
  • Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. 2024 PMID 38884260 PMC11317153 unsure
  • Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655 unsure
2 more
  • 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
  • Fedflow: cloud orchestration for federated learning with the FeatureCloud platform. 2026 PMID 42725323 PMC13561539
Details
Archive description

An increasing number of metagenomics researches found Gut microbiota (GM) were implicated with CRC. Here, we collected 168 fecal samples from Chong Qing CRC patients for studying the GM in Chinese typical population. We found that diet influenced CRC patients’ GM in composition and metabolic. Besides, specific species and gene fragments in CRC patients were discovered in familiar paired samples, and which were identified in other countries’ CRC patients.

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.scientific_name · “human gut metagenome”
  • body site study.description · “168 fecal samples from Chong Qing CRC patients”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN08329222age_at_collection_days15340.5R20.75external.cmd sourceage: 42; age_unit: Year; age_group: Adult
SAMN08329222antibiotic_exposurenoR20.75external.cmd sourceantibiotics_current_use: No
SAMN08329222bmi22.27R20.75external.cmd sourcebmi: 22.27
SAMN08329222collection_date2015-12-23R10.90biosample.attribute:collection_date2015-12-23
SAMN08329222countryCNR10.90sample.attr.geo_loc_nameChina: ChongQing
SAMN08329222health_conditioncolorectal_cancerR20.75external.cmd sourcedisease: colorectal cancer
SAMN08335927health_conditioncolorectal_cancerR20.75external.gmrepo sourcephenotype: Colorectal Neoplasms
SAMN08329222health_condition_detailcolorectal cancerR20.75external.cmd sourcedisease: colorectal cancer
SAMN08335927health_condition_detailColorectal NeoplasmsR20.75external.gmrepo sourcephenotype: Colorectal Neoplasms
SAMN08329222location_localityChongqingR10.85biosample.attribute:geo_loc_nameChina: ChongQing
SAMN08329222sexfemaleR20.75external.cmd sourcesex: Female
Sequencing

194 runs over 194 samples · mean 5.80 Gbp per run (median 5.77 Gbp, total 1,126.04 Gbp; 194 runs with a base count) · layout PAIRED 194 · platform ILLUMINA 194 · models HiSeq X Ten (194) · 88% of runs with a Sandpiper profile · first public 2019-01-02

Authors (62)

Zhu X first · Xu P · Zhu R · Gao W · Yin W · Lan P · Zhu L · Jiao N last · Wang S first · Jiang Y · Che L · Wang RH · Li SC last · Wang L first · Wang Q · Zhou Y last · Piccinno G first · Thompson KN · Manghi P · Ghazi AR · Thomas AM · Blanco-Míguez A · Asnicar F · Mladenovic K · Pinto F · Armanini F · Punčochář M · Piperni E · Heidrich V · Fackelmann G · Ferrero G · Tarallo S · Nguyen LH · Yan Y · Keles NA · Tuna BG · Vymetalkova V · Trompetto M · Liska V · Hucl T · Vodicka P · Bencsiková B · Čarnogurská M · Popovici V · Marmorino F · Cremolini C · Pardini B · Cordero F · Song M · Chan AT · Derosa L · Zitvogel L · Huttenhower C · Naccarati A · Budinska E · Segata N last · Weilguny L first · Probul N · Ren Y · Pons N · Baumbach J · Almeida M last

Downloads

PRJNA429097.csv.gz (7.0 KB) · parquet (79.8 KB) — all 194 samples, every field with route and confidence · PRJNA429097_determinations.csv.gz (17.6 KB) — 1,552 evidence rows

Samples (194 · every field this project has values for · hover a cell for its source)
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