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PRJNA1086048 SRP494885

Fecal metagenomes in IBD vs controls, Hong Kong, case-control

Metagenomic analysis of faecal microbiome as a tool for targeted non-invasive biomarkers for inflammatory bowel disease

1,154 fecal metagenome samples from Hong Kong, collected as a case-control study comparing subjects with inflammatory bowel disease to non-IBD controls to identify bacterial biomarkers for IBD diagnosis. machine-written summary

1,154 samples · 1,154 runs · HK · Age unknown · 2024 · 7.24 Gbp / sample

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Sources
✓Sequence archive 6,732✓Abstract / description 775○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 archive6,732 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id)
✓ Abstract / description775 sample values (health condition detail)
○ Full textread; no usable statement or table · PMC11645270
○ 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
Samples at a glance
1 sampling locations · 1 country
Age
unknown1,154
Condition
ulcerative_colitis205
crohns_disease174
Country
HK1,154
Body site
primary1,154
Collected 2015–2016
2015: 199 samples2016: 6 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 %)this project, 0.1–0.3 Gbp: 2 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 25 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 83 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 661 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 380 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 3 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 7.24 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolved

200 of 205 people sampled more than once (1,148 samples; median 7, up to 7 per person).

How longitudinal and relatedness information is derived

Community composition
Bifidobacterium 8.2%Blautia_A 7.8%Bacteroides 6.6%Phocaeicola 5.6%Faecalibacterium 4.0%Roseburia 3.6%Escherichia 3.3%Mediterraneibacter 2.7%Collinsella 2.6%Prevotella 2.3%Gemmiger 2.2%Anaerostipes 1.9%not assigned to a genus 3.6%other genera 45.8%

Genera, mean relative abundance over 1,011 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%
country1,154 100%1,154
health_condition379 33%379
subject_id1,153 100%1,153
detailed_location1,154 100%
health_condition_detail1,154 100%379775
latitude1,154 100%1,154
location_region1,154 100%1,154
longitude1,154 100%1,154
collection_date205 18%205
Papers (1)
Details
Archive description

This project collected and profiled paired shotgun metagenomes from subjects with inflammatory bowel disease (IBD) and non-IBD controls. We uncovered fecal bacterial markers for IBD and validated their accuracy in IBD diagnosis.

How this project entered the registry

Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • host run.scientific_name · “mouse gut metagenome”
  • body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN40355390collection_date2015-02R10.90biosample.attribute:collection_date2015-02
SAMN40355390countryHKR10.90sample.attr.geo_loc_nameHong Kong
SAMN40355390health_conditionulcerative_colitisR10.70sample.name_rule:aliasUC002
SAMN40355390health_condition_detailUCR10.70sample.name_rule:aliasUC002
SAMN43161825health_condition_detailmixed_case_control: inflammatory bowel disease patients vs non-IBD controlsR40.40study.descriptionsubjects with inflammatory bowel disease (IBD) and non-IBD controls
SAMN40355390latitude22.3200R10.90biosample.attribute:lat_lon22.32 N 114.17 E
SAMN40355390location_regionKowloon CityR10.60biosample.attribute:lat_lon22.32 N 114.17 E
SAMN40355390longitude114.1700R10.90biosample.attribute:lat_lon22.32 N 114.17 E
SAMN43161825subject_id1R10.85sample.attr.host_subject_id1
Sequencing

1,154 runs over 1,154 samples · mean 8.10 Gbp per run (median 7.24 Gbp, total 9,346.59 Gbp; 1,154 runs with a base count) · layout PAIRED 1,154 · platform ILLUMINA 1,154 · models Illumina NovaSeq 6000 (1,154) · 88% of runs with a Sandpiper profile · first public 2024-08-22 – 2024-08-31

Authors (22)

Zheng J first · Sun Q · Zhang M · Liu C · Su Q · Zhang L · Xu Z · Lu W · Ching J · Tang W · Cheung CP · Hamilton AL · Wilson O'Brien AL · Wei SC · Bernstein CN · Rubin DT · Chang EB · Morrison M · Kamm MA · Chan FKL · Zhang J · Ng SC last

Help complete this project

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

Downloads

PRJNA1086048.csv.gz (29.1 KB) · parquet (108.5 KB) — all 1,154 samples, every field with route and confidence · PRJNA1086048_determinations.csv.gz (51.8 KB) — 7,507 evidence rows

Samples (1,154 · every field this project has values for · hover a cell for its source)
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