Fecal microbiome in IBS vs controls, case-control, Ireland
139 fecal samples from adults in Ireland, comparing people with irritable bowel syndrome (including bile acid malabsorption) to matched controls, using shotgun and 16S sequencing; case-control design. machine-written summary
139 samples · 139 runs · IE · Adult · 2021 · 4.73 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 556 sample values (collection date, country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10154212, PMC11538712 |
| ○ 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 122 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 | 139 | 100% | ||||
| country | 139 | 100% | 139 | |||
| health_condition | 139 | 100% | 139 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 139 | 100% | 139 | |||
| health_condition_detail | 139 | 100% | 139 |
- Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption. 2020 PMID 31843589 own_data
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212 unsure
- Cross-Cohort Gut Microbiome Signatures of Irritable Bowel Syndrome Presentation and Treatment. 2024 PMID 39243395 PMC11538712 unsure
Archive description
Irritable bowel syndrome (IBS) is a heterogeneous disorder, but diagnoses and determination of subtypes are made based on symptoms. We profiled the fecal microbiomes of patients with and without IBS to identify biomarkers of this disorder. We collected fecal and urine samples from 80 patients with IBS (Rome IV criteria 16-70 years old) and 65 matched individuals without IBS (control individuals), along with anthropometric, medical, and dietary information. Shotgun and 16S ribosomal RNA amplicon sequencing were performed on feces.Patients with IBS had significant differences in network connections between diet and fecal microbiomes compared with control individuals these were accompanied by differences in fecal metabolomes. We did not find significant differences in fecal microbiota composition among patients with different IBS symptom subtypes. Despite the heterogeneity of IBS, patients have significant differences in urine and fecal metabolomes and fecal microbiome vs control individuals, independent of symptom-based subtypes of IBS.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “16-70 years old”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7756187 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA7756187 | country | IE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Ireland |
| SAMEA7756187 | health_condition | ibs | R1 | 0.70 | sample.name_rule:alias | Sample_WGS_IBS_S0049 |
| SAMEA7756187 | health_condition_detail | IBS | R1 | 0.70 | sample.name_rule:alias | Sample_WGS_IBS_S0049 |
Sequencing
139 runs over 139 samples · mean 4.89 Gbp per run (median 4.73 Gbp, total 679.79 Gbp; 139 runs with a base count) · layout PAIRED 139 · platform ILLUMINA 139 · models Illumina HiSeq 2500 (139) · 88% of runs with a Sandpiper profile · first public 2021-01-08
Authors (15)
Jeffery IB first · Das A · O'Herlihy E · Coughlan S · Cisek K · Moore M · Bradley F · Carty T · Pradhan M · Dwibedi C · Shanahan F · O'Toole PW last · Ghosh TS first · Li J first · Arendt E
Downloads
PRJEB42304.csv.gz (4.0 KB) · parquet (74.3 KB) — all 139 samples, every field with route and confidence · PRJEB42304_determinations.csv.gz (4.4 KB) — 556 evidence rows