Metagenomes in Crohn's disease requiring resection, Belgium
98 gut metagenome samples from adult Crohn's disease patients who required resection, from a case-control cohort in Leuven, Belgium. machine-written summary
98 samples · 98 runs · BE · Adult · 2022 · 16.22 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 784 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 98 sample values (location site) · PMC8665270 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 196 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
49 of 49 people sampled more than once (98 samples; median 2, up to 2 per person) · follow-up median 6 mo (max 6 mo) · median interval between samples 6 mo (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Samples collected at baseline (post-surgery, timepoint 0) and at month 6 post-surgery” (time origin: surgery); stated follow-up 6 mo.
Each row is one person (36 shown of 49); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 88 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 | 98 | 100% | ||||
| country | 98 | 100% | 98 | |||
| health_condition | 98 | 100% | 98 | |||
| subject_id | 98 | 100% | 98 | |||
| collection_date | 98 | 100% | 98 | |||
| detailed_location | 98 | 100% | ||||
| health_condition_detail | 98 | 100% | 98 | |||
| latitude | 98 | 100% | 98 | |||
| location_locality | 98 | 100% | 98 | |||
| location_region | 98 | 100% | 98 | |||
| location_site | 98 | 100% | 98 | |||
| longitude | 98 | 100% | 98 | |||
| timepoint_label | 98 | 100% | 98 |
- Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach 2021 PMID 34938418 PMC8665270 own_data
Archive description
Metagenomes of the gut microbiota of CD patients that required resection from a Belgian cohort, used in Serrano-Gomez, Gerard et al. 'Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach.' Computational and structural biotechnology journal vol. 19 6481-6489. 2 Dec. 2021, doi:10.1016/j.csbj.2021.11.037
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Metagenomes of the gut microbiota of CD”
- body site study.description · “Metagenomes of the gut microbiota of CD”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN29232651 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN29232651 | country | BE | R1 | 0.90 | sample.attr.geo_loc_name | Belgium:Leuven |
| SAMN29232651 | health_condition | crohns_disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN29232651 | health_condition_detail | Crohn Disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN29232651 | latitude | 50.8786 | R1 | 0.90 | biosample.attribute:lat_lon | 50.87857130 N 4.67430330 E |
| SAMN29232651 | location_locality | Leuven | R1 | 0.85 | biosample.attribute:geo_loc_name | Belgium:Leuven |
| SAMN29232651 | location_region | Flanders | R1 | 0.60 | biosample.attribute:lat_lon | 50.87857130 N 4.67430330 E |
| SAMN29232651 | location_site | University Hospital Leuven | R3 | 0.70 | paper.fulltext.methods | Belgian cohort recruited at the University Hospital Leuven |
| SAMN29232651 | longitude | 4.6743 | R1 | 0.90 | biosample.attribute:lat_lon | 50.87857130 N 4.67430330 E |
| SAMN29232651 | subject_id | 02 | R1 | 0.70 | sample.name_rule:alias | P02_Fc_0 |
| SAMN29232651 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:alias | P02_Fc_0 |
Sequencing
98 runs over 98 samples · mean 16.46 Gbp per run (median 16.22 Gbp, total 1,613.03 Gbp; 98 runs with a base count) · layout PAIRED 98 · platform ILLUMINA 98 · models Illumina HiSeq X (98) · 90% of runs with a Sandpiper profile · first public 2022-06-29 – 2022-09-30
Authors (12)
Serrano-Gómez G first · Mayorga L · Oyarzun I · Roca J · Borruel N · Casellas F · Varela E · Pozuelo M · Machiels K · Guarner F · Vermeire S · Manichanh C last
Downloads
PRJNA851554.csv.gz (3.7 KB) · parquet (74.8 KB) — all 98 samples, every field with route and confidence · PRJNA851554_determinations.csv.gz (8.7 KB) — 1,078 evidence rows