Crohn's disease mucosa microbiota, Australia, case-control
58 samples from post-operative Crohn's disease patients in Australia, analyzed using combined microbe culture and metagenomic sequencing (MC-MGS) of mucosa-associated tissue, in a case-control design. machine-written summary
58 samples · 58 runs · AU · Age unknown · 2021 · 3.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 227 sample values (country, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8528831 |
| ✓ Supplementary tables | 15 sample values (age, sex, subject id) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
5 of 7 people sampled more than once (16 samples; median 3, up to 4 per person).
Genera, mean relative abundance over 16 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 5 | 9% | ||||
| country | 58 | 100% | 58 | |||
| health_condition | 58 | 100% | 58 | |||
| subject_id | 58 | 100% | 53 | 5 | ||
| health_condition_detail | 58 | 100% | 58 | |||
| age_at_collection_days | 5 | 9% | 5 | |||
| sex | 5 | 9% | 5 |
- Novel strain-level resolution of Crohn's disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing. 2021 PMID 34035441 PMC8528831 own_data
Archive description
Use of a novel ex vivo approach combining microbe culture from anaerobically preserved tissue with metagenome sequencing to reveal patient-specific and strain-level differences among bacterial communities in post-operative Crohns disease patients
How this project entered the registry
Classified as human gut / stool / other human site 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 · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- body site sample.attr.env_medium · “Mucosal Tissue (n=40/58)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18499172 | age_at_collection_days | 27759.0 | R2 | 0.80 | paper.supp.41396_2021_991_MOESM1_ESM.docx[table1!Age] | Age: 76 |
| SAMN18499163 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia |
| SAMN18499163 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:isolation_source | isolation_source: mucosal tissue from Crohns disease patient |
| SAMN18499164 | health_condition | crohns_disease | R1 | 0.70 | sample.name_rule:title | CD10_ANA_Biopsy |
| SAMN18499163 | health_condition_detail | mucosal tissue from Crohns disease patient | R1 | 0.85 | biosample.attribute:isolation_source | isolation_source: mucosal tissue from Crohns disease patient |
| SAMN18499164 | health_condition_detail | CD | R1 | 0.70 | sample.name_rule:title | CD10_ANA_Biopsy |
| SAMN18499172 | sex | female | R2 | 0.80 | paper.supp.41396_2021_991_MOESM1_ESM.docx[table1!Gender] | Gender: Female |
| SAMN18499163 | subject_id | 10 | R1 | 0.70 | sample.name_rule:title | CD10_ANA_2MC_M2Host |
| SAMN18499172 | subject_id | CD10 | R2 | 0.80 | paper.supp.41396_2021_991_MOESM1_ESM.docx[table1!ID] | ID: CD10 |
Sequencing
58 runs over 58 samples · mean 3.60 Gbp per run (median 3.69 Gbp, total 209.06 Gbp; 58 runs with a base count) · layout PAIRED 58 · platform ILLUMINA 58 · models Illumina MiSeq (58) · 88% of runs with a Sandpiper profile · first public 2021-04-13
Authors (15)
Teh JJ first · Berendsen EM · Hoedt EC · Kang S · Zhang J · Zhang F · Liu Q · Hamilton AL · Wilson-O'Brien A · Ching J · Sung JJY · Yu J · Ng SC · Kamm MA · Morrison M last
Downloads
PRJNA715634.csv.gz (2.3 KB) · parquet (71.2 KB) — all 58 samples, every field with route and confidence · PRJNA715634_determinations.csv.gz (2.6 KB) — 242 evidence rows