Gut microbiota in IBD & circadian rest-activity disruption
Cross-sectional study of 41 stool samples from USA patients with ulcerative colitis or Crohn's disease, examining links between circadian rest-activity misalignment, intestinal permeability, and gut microbiota composition. machine-written summary
41 samples · 41 runs · US · Age unknown · 2020 · 2.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 164 sample values (collection date, country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 41 sample values (location locality) · PMC8900134 |
| ○ 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 |
Genera, mean relative abundance over 37 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 | 41 | 100% | 41 | |||
| health_condition | 41 | 100% | 41 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 41 | 100% | 41 | |||
| detailed_location | 41 | 100% | ||||
| health_condition_detail | 41 | 100% | 41 | |||
| location_locality | 41 | 100% | 41 |
- Disrupted Circadian Rest-Activity Cycles in Inflammatory Bowel Disease Are Associated With Aggressive Disease Phenotype, Subclinical Inflammation, and Dysbiosis. 2021 PMID 35265631 PMC8900134 own_data
Archive description
Crohn’s Disease (CD) and Ulcerative Colitis (UC), collectively known as inflammatory bowel disease (IBD), are two of the most significant chronic conditions of the gastrointestinal tract (GIT). IBD is typically diagnosed at an early age, has no known cure, and has a chronic relapsing and remitting disease course that includes disabling symptoms during periodic flare ups. IBD affects over 1.5 million individuals in the US with an estimated direct cost of $6.1 billion.(1) IBD has a highly variable disease course, and identifying factors to avoid disease flare is essential to avoid complications such as</p><p>hospitalization and surgery. Recently there has been compelling evidence that IBD subjects commonly have disrupted sleep, and disrupted sleep leads to a more aggressive disease course.(2, 3) Sleep and multiple biological processes in the body are orchestrated by the central circadian clock located in the suprachiasmatic nucleus. We have shown that disruption of the light:dark cycle, or circadian misalignment, can be a risk factor for increased intestinal permeability, dysbiosis, and mucosal inflammation, all of which are known risk factors for disease flare in IBD. However, whether circadian misalignment is prevalent in IBD or if it is a factor in promoting disease flare is a gap in our current knowledge. Microbiome analysis will be conducted to determine these primary outcome measures.
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 study.description · “chronic conditions of the gastrointestinal tract”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN13012336 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN13012336 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN13012336 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | Ulcerative Colitis |
| SAMN13012336 | health_condition_detail | Ulcerative Colitis | R1 | 0.90 | sample.attr.host_disease | Ulcerative Colitis |
| SAMN13012336 | location_locality | Chicago | R3 | 0.70 | paper.fulltext.methods | Rush University Medical Center |
Sequencing
41 runs over 41 samples · mean 2.07 Gbp per run (median 2.10 Gbp, total 84.78 Gbp; 41 runs with a base count) · layout PAIRED 41 · platform ILLUMINA 41 · models Illumina HiSeq 4000 (41) · 90% of runs with a Sandpiper profile · first public 2020-11-02
Authors (13)
Swanson GR first · Kochman N · Amin J · Chouhan V · Yim W · Engen PA · Shaikh M · Naqib A · Tran L · Voigt RM · Forsyth CB · Green SJ · Keshavarzian A last
Downloads
PRJNA576887.csv.gz (1.8 KB) · parquet (70.5 KB) — all 41 samples, every field with route and confidence · PRJNA576887_determinations.csv.gz (1.6 KB) — 205 evidence rows