Gut microbiota and depression/fatigue in active IBD
Cross-sectional study of 62 stool samples from adults with active inflammatory bowel disease, examining associations between gut microbiota composition/function and self-reported depression and fatigue severity. machine-written summary
62 samples · 62 runs · DE · Adult · 2022 · 6.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 496 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, location locality, location site, subject id) · PMC9575298 |
| ○ 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 53 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 | 62 | 100% | ||||
| country | 62 | 100% | 62 | |||
| health_condition | 62 | 100% | 62 | |||
| subject_id | 62 | 100% | 62 | |||
| antibiotic_exposure | 62 | 100% | 62 | |||
| collection_date | 62 | 100% | 62 | |||
| detailed_location | 62 | 100% | ||||
| health_condition_detail | 62 | 100% | 62 | |||
| location_locality | 62 | 100% | 62 | |||
| location_site | 62 | 100% | 62 |
- Depression and fatigue in active IBD from a microbiome perspective-a Bayesian approach to faecal metagenomics. 2022 PMID 36244970 PMC9575298 own_data
Archive description
Extraintestinal symptoms are common in inflammatory bowel diseases (IBD) and include depression and fatigue. These are highly prevalent especially in active disease, potentially due to inflammation-mediated changes in the microbiota-gut-brain-axis. The aim of this study was to investigate associations between structural and functional microbiota characteristics and severity of fatigue and depressive symptoms in patients with active IBD. We included clinical data of 62 prospectively enrolled patients with IBD in an active disease state. Patients supplied stool samples and completed questionnaires regarding depression and fatigue symptoms. Based on taxonomical and functional metagenomic annotations of faecal gut microbiota, we investigated associations between bacterial genera/functional (KEGG-)modules and symptom severity of self-reported fatigue and depression by means of a bayesian triple association approach. Triple associations with moderate to strong evidence were found for 3 genera (Odoribacter, Anaerotruncus and Alistipes) and 3 functional modules (pectin-, glycosaminoglycan- and central carbohydrate metabolism) with regard to depression, and for 4 genera (Intestinimonas, Anaerotruncus, Eubacterium and Clostridiales g.i.s) and 2 functional modules implicating amino acid and central carbohydrate metabolism with regard to fatigue. This study provides first evidence of a triple association between microbiota composition, function and extraintestinal symptoms in active IBD. Depression and fatigue were associated with lower abundances of short chain fatty acid-producers and distinct pathways implicating glycan-, carbohydrate and amino acid metabolism. Our results suggest that microbiota-directed therapeutic approaches may reduce fatigue and depression in IBD and should be investigated in future research.
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.description · “in the microbiota- gut -brain-axis. The aim”
- body site external_curation.infant_catalog · “body_site_call gut”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA10835160 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods | Patients with recent use of antibiotics (< 4 weeks before recruitment) were excluded from the study. |
| SAMEA10835160 | collection_date | 2018-01/2019-10 | R3 | 0.70 | paper.body.methods | between January 2018 and October 2019 |
| SAMEA10835160 | country | DE | R3 | 0.70 | paper.body.methods | recruited from the IBD outpatient unit at Department of Medicine II, Medical Faculty Mannheim, Heidelberg University |
| SAMEA10835160 | health_condition | ibd_unspecified | R3 | 0.70 | paper.abstract | clinical data of 62 prospectively enrolled patients with IBD in an active disease state |
| SAMEA10835160 | health_condition_detail | active IBD | R3 | 0.70 | paper.abstract | clinical data of 62 prospectively enrolled patients with IBD in an active disease state |
| SAMEA10835160 | location_locality | Mannheim | R3 | 0.70 | paper.body.methods | recruited from the IBD outpatient unit at Department of Medicine II, Medical Faculty Mannheim, Heidelberg University |
| SAMEA10835160 | location_site | Department of Medicine II, Medical Faculty Mannheim, Heidelberg University | R3 | 0.70 | paper.body.methods | recruited from the IBD outpatient unit at Department of Medicine II, Medical Faculty Mannheim, Heidelberg University |
| SAMEA10835160 | subject_id | SAMEA10835160 | R3 | 0.75 | design.one_sample_per_subject:fulltext | The cross-sectional design and the undirected and correlative nature of the analysed joint network do |
Sequencing
62 runs over 62 samples · mean 7.16 Gbp per run (median 6.96 Gbp, total 443.98 Gbp; 62 runs with a base count) · layout PAIRED 62 · platform ILLUMINA 62 · models Illumina HiSeq 2000 (62) · 87% of runs with a Sandpiper profile · first public 2022-09-18
Authors (0)
No author record.
Downloads
PRJEB49262.csv.gz (2.6 KB) · parquet (72.9 KB) — all 62 samples, every field with route and confidence · PRJEB49262_determinations.csv.gz (4.2 KB) — 496 evidence rows