Home › Studies › PRJNA1251707
PRJNA1251707 SRP579189

Gut metagenomes for IBD live biotherapeutic discovery, Brisbane

Metagenomes for rational identification of live biotherapeutics for the treatment of inflammatory bowel disease

312 gut metagenome samples from Brisbane, Australia, generated to identify microbial species depleted in inflammatory bowel disease (IBD) as candidate live biotherapeutic products; study design and participant health status are not specified in the curated facts. machine-written summary

312 samples · 312 runs · AU · Age unknown · 2025 · 5.30 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 2,496○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 archive2,496 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
○ Abstract / descriptionread; no usable statement
– Full textno open-access full text linked
– Supplementary tablesno supplementary tables available (or none open access)
– 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
unknown312
Condition
healthy_control235
ulcerative_colitis46
crohns_disease28
ibd_unspecified3
Country
AU312
Body site
primary312
Collected 2018–2019
2018: 170 samples2019: 142 samples20182019
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: 311 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 1 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 5.30 Gbp per sample0130Gbp
Community composition
Faecalibacterium 8.2%Bacteroides 7.6%Prevotella 6.5%Alistipes 5.4%Phocaeicola 5.3%Roseburia 3.7%Blautia_A 3.5%Vescimonas 1.7%Gemmiger 1.7%Ruminococcoides 1.7%Lachnospira 1.7%Fusicatenibacter 1.5%not assigned to a genus 7.0%other genera 44.6%

Genera, mean relative abundance over 310 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%
country312 100%312
health_condition312 100%312
subject_id0 0%
collection_date312 100%312
detailed_location312 100%
health_condition_detail312 100%312
latitude312 100%312
location_locality312 100%312
location_region312 100%312
longitude312 100%312
Papers (1)
  • A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics 2024 own_data
Details
Archive description

This project aimed to develop a rational, metagenomics-guided pipeline for the discovery of live biotherapeutic products (LBPs) targeting microbiome-associated diseases, with a focus on Inflammatory Bowel Disease (IBD). Using large-scale metagenomic datasets from healthy and disease cohorts, we sought to identify microbial species that are consistently depleted in IBD and prioritize them as therapeutic candidates.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN48021155collection_date2018-09-09R10.90biosample.attribute:collection_date2018-09-09
SAMN48021155countryAUR10.90sample.attr.geo_loc_nameAustralia: Brisbane
SAMN48021155health_conditionhealthy_controlR10.85biosample.attribute:titleHealthy
SAMN48021155health_condition_detailHealthyR10.85biosample.attribute:titleHealthy
SAMN48021155latitude-27.4705R10.90biosample.attribute:lat_lon27.4705 S 153.0260 E
SAMN48021155location_localityBrisbaneR10.85biosample.attribute:geo_loc_nameAustralia: Brisbane
SAMN48021155location_regionQueenslandR10.60biosample.attribute:lat_lon27.4705 S 153.0260 E
SAMN48021155longitude153.0260R10.90biosample.attribute:lat_lon27.4705 S 153.0260 E
Sequencing

312 runs over 312 samples · mean 5.36 Gbp per run (median 5.30 Gbp, total 1,672.34 Gbp; 312 runs with a base count) · layout PAIRED 312 · platform ILLUMINA 312 · models Illumina NovaSeq 6000 (312) · 99% of runs with a Sandpiper profile · first public 2025-04-18

Authors (0)

No author record.

Help complete this project

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

Downloads

PRJNA1251707.csv.gz (8.6 KB) · parquet (81.9 KB) — all 312 samples, every field with route and confidence · PRJNA1251707_determinations.csv.gz (15.6 KB) — 2,496 evidence rows

Samples (312 · every field this project has values for · hover a cell for its source)
Loading the sample table…