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PRJNA1079906 SRP491482

Fecal metagenomes in colorectal cancer, Gansu, China

Fecal microbiome sequencing of colorectal cancer

133 fecal samples from healthy individuals, adenoma patients, and colorectal cancer patients in Gansu, China, analyzed by metagenomic sequencing in a case-control design to study colorectal cancer-associated microbiome alterations. machine-written summary

133 samples · 133 runs · CN · Age unknown · 2024 · 11.47 Gbp / sample

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Sources
✓Sequence archive 931○Abstract / description○Full text○Supplementary tables–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive931 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC12090784, PMC12326762, PMC12376641
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

design observational_with_procedure

Samples at a glance
1 sampling locations · 1 country
Age
unknown133
Condition
healthy_control55
colorectal_cancer40
colorectal_adenoma38
Country
CN133
Body site
primary133
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: 8 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 125 samplesall 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 11.47 Gbp per sample0130Gbp
Community composition
Bacteroides 15.2%Phocaeicola 13.4%Faecalibacterium 5.3%Prevotella 5.1%Alistipes 4.2%Escherichia 3.8%Roseburia 3.7%Ruminococcoides 2.2%Parabacteroides 2.1%Megamonas 1.8%Mediterraneibacter 1.7%Fimenecus 1.7%not assigned to a genus 2.7%other genera 37.0%

Genera, mean relative abundance over 121 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country133 100%133
health_condition133 100%133
subject_id0 0%
collection_date133 100%133
detailed_location133 100%
health_condition_detail133 100%133
latitude133 100%133
location_region133 100%133
longitude133 100%133
Papers (3)
  • Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control. 2025 PMID 40433987 PMC12376641 own_data
  • Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study. 2025 PMID 40298367 PMC12090784 unsure
  • Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer. 2025 PMID 40770383 PMC12326762 unsure
Details
Archive description

To faciliate colorectal cancer (CRC) early diagnosis, fecal samples from healthy people, adenoma patients and CRC patients were collected and subjected to metagenome sequencing on llumina Novaseq 6000 platform.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.

  • host study.description · “healthy people, adenoma patients and CRC patients”
  • body site study.title · “Fecal microbiome sequencing of colorectal cancer”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN40094910collection_date2023-11-11R10.90biosample.attribute:collection_date2023-11-11
SAMN40094910countryCNR10.90sample.attr.geo_loc_nameChina: Gansu
SAMN40094910health_conditionhealthy_controlR10.70sample.name_rule:sample_aliasFMGH01
SAMN40094910health_condition_detailHR10.70sample.name_rule:sample_aliasFMGH01
SAMN40094910latitude35.5700R10.90biosample.attribute:lat_lon35.57 N 102.59 E
SAMN40094910location_regionGansuR10.85biosample.attribute:geo_loc_nameChina: Gansu
SAMN40094910longitude102.5900R10.90biosample.attribute:lat_lon35.57 N 102.59 E
Sequencing

133 runs over 133 samples · mean 11.28 Gbp per run (median 11.47 Gbp, total 1,500.83 Gbp; 133 runs with a base count) · layout PAIRED 133 · platform ILLUMINA 133 · models Illumina NovaSeq 6000 (133) · 91% of runs with a Sandpiper profile · first public 2024-03-24

Authors (24)

Zhou Z first · Ma Y · Zhang D · Ji R · Wang Y · Zhao J · Ma C · Zhu H · Shen H · Jiang X · Niu Y · Lu J · Zhang B · Tu L · Zhang H · Ma X · Chen P last · Yang M · Fang H · Li Y · Liu Y · Cheng Z · Zhao Y · Si Z

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata

Downloads

PRJNA1079906.csv.gz (4.0 KB) · parquet (74.8 KB) — all 133 samples, every field with route and confidence · PRJNA1079906_determinations.csv.gz (6.5 KB) — 931 evidence rows

Samples (133 · every field this project has values for · hover a cell for its source)
Loading the sample table…