Gut microbiome in Crohn's disease after stem cell transplant
28 longitudinal stool metagenome samples from Crohn's disease/IBD patients undergoing autologous hematopoietic stem cell transplantation (involving surgery), plus corresponding humanised mouse model samples, studying links between microbiota, metabolites and sulfur metabolism. machine-written summary
10 samples · 28 runs · ES · Age unknown · 2020 · 6.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 27 sample values (health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 33 sample values (country, health condition, location locality, location site) · PMC7456324 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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
Surgical procedure studied before/after (bariatric surgery design single_arm_before_after · population crohns_disease · Autologous hematopoietic stem cell transplantation, stool sampled longitudinally over 5 years
“undergoing autologous hematopoietic stem cell transplantation” — abstract:32859898 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
3 of 3 people sampled more than once (10 samples; median 4, up to 4 per person). Schedule stated by the source: “Baseline (pre-HSCT), week 26 (T26), week 52 (T52) post-transplant, plus variable additional timepoints up to 5 years” (time origin: transplant); stated follow-up 5.0 y.
Genera, mean relative abundance over 24 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 | 0 | 0% | ||||
| country | 10 | 100% | 10 | |||
| health_condition | 10 | 100% | 7 | 3 | ||
| subject_id | 10 | 100% | 10 | |||
| detailed_location | 10 | 100% | ||||
| health_condition_detail | 10 | 100% | 10 | |||
| location_locality | 10 | 100% | 10 | |||
| location_site | 10 | 100% | 10 |
- Integrated microbiota and metabolite profiles link Crohn's disease to sulfur metabolism. 2020 PMID 32859898 PMC7456324 own_data
Archive description
The project involves an integrative multi-omics analysis of 30 Crohn’s disease patients after autologous hematopoietic stem cell transplantation (HSCT), with stool samples longitudinally collected over 5 years. The metagenome data here represents the gut microbiome from the selected samples from the cohort and ther corresponding humanised mouse models.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host study.description · “30 Crohn’s disease patients”
- host run.scientific_name · “mouse gut metagenome”
- host study.description · “corresponding humanised mouse models”
- body site study.description · “stool samples longitudinally collected”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12879219 | country | ES | R3 | 0.70 | paper.fulltext.methods | recruited at the Department of Gastroenterology, Hospital Clinic Barcelona |
| SAMN12879219 | health_condition | ibd_unspecified | R1 | 0.60 | biosample_attr | Remission-Responder |
| SAMN12879220 | health_condition | crohns_disease | R3 | 0.70 | paper.fulltext.methods | fecal samples from 29 patients with up to 5-year follow-up |
| SAMN12879219 | health_condition_detail | Remission-Responder | R1 | 0.90 | sample.attr.donor_disease_status | Remission-Responder |
| SAMN12879219 | location_locality | Barcelona | R3 | 0.70 | paper.fulltext.methods | Hospital Clinic Barcelona |
| SAMN12879219 | location_site | Hospital Clinic Barcelona | R3 | 0.70 | paper.fulltext.methods | recruited at the Department of Gastroenterology, Hospital Clinic Barcelona |
| SAMN12879219 | subject_id | P16 | R1 | 0.85 | sample.attr.patient_number | P16 |
Sequencing
28 runs over 10 samples · mean 9.69 Gbp per run (median 6.70 Gbp, total 271.24 Gbp; 28 runs with a base count) · layout PAIRED 28 · platform ILLUMINA 28 · models Illumina HiSeq 2500 (28) · 86% of runs with a Sandpiper profile · first public 2020-06-02
Authors (15)
Metwaly A first · Dunkel A · Waldschmitt N · Raj ACD · Lagkouvardos I · Corraliza AM · Mayorgas A · Martinez-Medina M · Reiter S · Schloter M · Hofmann T · Allez M · Panes J · Salas A · Haller D last
Downloads
PRJNA575186.csv.gz (1.2 KB) · parquet (69.8 KB) — all 10 samples, every field with route and confidence · PRJNA575186_determinations.csv.gz (1.1 KB) — 60 evidence rows