Gut microbiota in Crohn's disease, case-control study
A case-control study of 34 gut microbiome samples comparing individuals with Crohn's disease (27 samples) to healthy controls (7 samples); sample countries and ages are largely unrecorded. machine-written summary
34 samples · 64 runs · Age unknown · 2010 · 0.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 136 sample values (health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC4269443, PMC4883586, PMC5057277, PMC5902703, PMC6215618, PMC6558107, PMC7038607, PMC9163076 |
| ○ 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 |
longitudinal — not resolved
12 of 17 people sampled more than once (29 samples; median 2, up to 3 per person). Schedule stated by the source: “Same gap_subject_id appears on multiple samples with different library_name collection dates (e.g. subject 571515: 20111130 and 20111209); no stated interval or visit labels.”.
Genera, mean relative abundance over 15 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 | 0 | 0% | ||||
| health_condition | 34 | 100% | 34 | |||
| subject_id | 34 | 100% | 34 | |||
| health_condition_detail | 34 | 100% | 34 | |||
| sex | 34 | 100% | 34 |
- Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. 2016 PMID 27239563 PMC4883586 own_data
- The Presence of Genotoxic and/or Pro-inflammatory Bacterial Genes in Gut Metagenomic Databases and Their Possible Link With Inflammatory Bowel Diseases. 2018 PMID 29692798 PMC5902703 own_data
- What we can see from very small size sample of metagenomic sequences. 2018 PMID 30390617 PMC6215618 own_data
- Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes. 2014 PMID 25517115 PMC4269443 unsure
- FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies. 2016 PMID 27724866 PMC5057277 unsure
3 more
- Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis. 2019 PMID 31214144 PMC6558107
- Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. 2020 PMID 32093762 PMC7038607
- Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. 2022 PMID 35654877 PMC9163076
Archive description
This study aims to unravel the contribution of the bacteria that normally inhabit the human gastrointestinal tract to Crohn's disease by using a multidisciplinary approach to study changes in the structure and function of gut microbial communities in three sets of patient cohorts who have Crohn's disease. These results will be compared with those obtained from the study of healthy individuals and have the potential to identify new biomarkers of disease severity, location, and progression.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- host study.title · “Human Gut Microbiota in Crohn's Disease”
- body site study.title · “Human Gut Microbiota”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN00022438 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | Crohn Disease |
| SAMN00022453 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:subject_is_affected | subject_is_affected: No |
| SAMN00022438 | health_condition_detail | Crohn Disease | R1 | 0.90 | sample.attr.study_disease | Crohn Disease |
| SAMN00022438 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN00022438 | subject_id | 276384 | R1 | 0.85 | sample.attr.gap_subject_id | 276384 |
Sequencing
64 runs over 34 samples · mean 4.22 Gbp per run (median 0.27 Gbp, total 270.35 Gbp; 64 runs with a base count) · layout SINGLE 48, PAIRED 16 · platform LS454 48, ILLUMINA 16 · models 454 GS FLX Titanium (48), Illumina HiSeq 2000 (16) · 25% of runs with a Sandpiper profile · first public 2010-06-15 – 2012-06-21
Authors (33)
Kim J first · Kim MS · Koh AY · Xie Y · Zhan X last · Roche-Lima A first · Carrasquillo-Carrión K · Gómez-Moreno R · Cruz JM · Velázquez-Morales DM · Rogozin IB · Baerga-Ortiz A last · Kwak J first · Park J last · Dai D first · Wang T · Wu S · Gao NL · Chen WH last · Stockdale SR first · Harrington RS · Shkoporov AN · Khokhlova EV · Daly KM · McDonnell SA · O'Reagan O · Nolan JA · Sheehan D · Lavelle A · Draper LA · Shanahan F · Ross RP · Hill C last
Downloads
PRJNA46321.csv.gz (1.7 KB) · parquet (70.0 KB) — all 34 samples, every field with route and confidence · PRJNA46321_determinations.csv.gz (1.2 KB) — 136 evidence rows