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PRJNA725613 SRP318275

Colorectal disease gut microbiota case-control, Zhengzhou

colorectal gut microbiota

16 fecal samples from patients with adenoma, colorectal cancer, or hemorrhoids in Zhengzhou, China, profiled by 16S rRNA amplicon and shallow metagenomic sequencing in a case-control design. machine-written summary

16 samples · 16 runs · CN · Age unknown · 2021 · 1.11 Gbp / sample

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Sources
✓Sequence archive 112○Abstract / description✓Full text 48✓Supplementary tables 32–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive112 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude)
○ Abstract / descriptionread; no usable statement
✓ Full text48 sample values (location region, location site, subject id) · PMC8299945
✓ Supplementary tables32 sample values (age, sex)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
adult12
elderly3
unknown1
Condition
colorectal_adenoma6
other_disease6
colorectal_cancer4
Sex
male9
female7
Country
CN16
Body site
primary16
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 %)this project, 0.3–1 Gbp: 8 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 5 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 3 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 1.11 Gbp per sample0130Gbp
Community composition
Prevotella 23.5%Phocaeicola 20.4%Bacteroides 9.3%Escherichia 4.1%Faecalibacterium 3.1%Streptococcus 2.7%Klebsiella 2.2%Lachnospira 1.6%Veillonella 1.4%Megamonas 1.2%Enterocloster 1.2%Roseburia 1.1%not assigned to a genus 8.9%other genera 19.3%

Genera, mean relative abundance over 15 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category15 94%
country16 100%16
health_condition16 100%16
subject_id16 100%16
age_at_collection_days16 100%16
collection_date16 100%16
detailed_location16 100%
health_condition_detail16 100%16
latitude16 100%16
location_locality16 100%16
location_region16 100%16
location_site16 100%16
longitude16 100%16
sex16 100%16
Papers (1)
  • Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing. 2021 PMID 34307461 PMC8299945 own_data
Details
Archive description

Exploring potential key drivers of gut microbes in patients with colorectal disease with 16S amplicon and metagenomics

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN18895703age_at_collection_days26298.0R20.80paper.supp.DataSheet1.docx[table1!Age]72
SAMN18895703collection_date2019-10R10.90biosample.attribute:collection_date2019-10
SAMN18895703countryCNR10.90sample.attr.geo_loc_nameChina:Zhengzhou
SAMN18895703health_conditioncolorectal_adenomaR10.70sample.name_rule:aliasAdenoma_A1
SAMN18895703health_condition_detailAdenomaR10.70sample.name_rule:aliasAdenoma_A1
SAMN18895703latitude34.8000R10.90biosample.attribute:lat_lon34.80 N 113.76 E
SAMN18895703location_localityZhengzhouR10.85biosample.attribute:geo_loc_nameChina:Zhengzhou
SAMN18895703location_regionHenan ProvinceR30.70paper.fulltext.methodsZhengzhou, Henan Province, China
SAMN18895703location_siteFirst Affiliated Hospital, Zhengzhou UniversityR30.70paper.fulltext.methodsFirst Affiliated Hospital, Zhengzhou University
SAMN18895703longitude113.7600R10.90biosample.attribute:lat_lon34.80 N 113.76 E
SAMN18895703sexmaleR20.80paper.supp.DataSheet1.docx[table1!Gender]Male
SAMN18895703subject_idSAMN18895703R30.75design.one_sample_per_subject:fulltextA total of 16 fecal samples were collected from 16 hospitalized patients.
Sequencing

16 runs over 16 samples · mean 1.60 Gbp per run (median 1.11 Gbp, total 25.61 Gbp; 16 runs with a base count) · layout PAIRED 16 · platform ILLUMINA 16 · models Illumina NovaSeq 6000 (16) · 94% of runs with a Sandpiper profile · first public 2021-08-27

Authors (6)

Liu Y first · Li X · Yang Y · Wang S · Ji B · Wei Y last

Downloads

PRJNA725613.csv.gz (1.5 KB) · parquet (72.0 KB) — all 16 samples, every field with route and confidence · PRJNA725613_determinations.csv.gz (2.5 KB) — 192 evidence rows

Samples (16 · every field this project has values for · hover a cell for its source)
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