IBS-D vs bile acid diarrhoea gut microbiome, Minnesota
194 stool samples from Minnesota, USA, in a case-control study comparing patients with IBS-D (irritable bowel syndrome with diarrhoea) to those with bile acid diarrhoea, examining microbial dysbiosis and mucosal gene expression. machine-written summary
194 samples · 194 runs · US · Age unknown · 2025 · 8.54 Gbp / sample
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what each source gave
| ✓ Sequence archive | 1,358 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| – Abstract / description | no abstract or project description |
| ✓ Full text | 388 sample values (location locality, location site) · PMC9669287 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 187 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 | 194 | 100% | 194 | |||
| health_condition | 194 | 100% | 194 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 194 | 100% | 194 | |||
| detailed_location | 194 | 100% | ||||
| health_condition_detail | 194 | 100% | 194 | |||
| latitude | 194 | 100% | 194 | |||
| location_locality | 194 | 100% | 194 | |||
| location_region | 194 | 100% | 194 | |||
| location_site | 194 | 100% | 194 | |||
| longitude | 194 | 100% | 194 |
- Comparison of biochemical, microbial and mucosal mRNA expression in bile acid diarrhoea and irritable bowel syndrome with diarrhoea. 2023 PMID 35580964 PMC9669287 own_data
Archive description
Objective There are altered mucosal functions in irritable bowel syndrome with diarrhoea (IBS-D) ~30% of patients with IBS-D have abnormal bile acid (BA) metabolism (ABAM) and diarrhoea (summarised as BAD).</p><p>Aim To compare biochemical parameters, gastrointestinal and colonic transit, rectal sensation and pathobiological mechanisms in IBS-D without ABAM and in BAD (serum 7C4>52 ng/mL).</p><p>Design In patients with Rome III criteria of IBS-D, we compared biochemical features, colonic transit, rectal sensation, deep genotype of five BA-related genes, ileal and colonic mucosal mRNA (differential expression (DE) analysis) and stool dysbiosis (including functional analysis of microbiome). Results in BAD were compared with IBS-D without ABAM.</p><p>Results Compared with 161 patients with IBS-D without ABAM, 44 patients with BAD had significantly faster colonic transit, lower microbial alpha diversity, different compositional profile (beta diversity) and higher Firmicutes to Bacteroidetes ratio with evidence of decreased expression of bile acid thiol ligase (involved in transformation of primary to secondary BAs) and decreased sulfatases. In BAD (compared with IBS-D without ABAM), terminal ileal biopsies showed downregulation of SLC44A5 (a BA transporter), and ascending colon biopsies showed upregulation in barrier-weakening genes (CLDN2), serine protease inhibitors, immune activation, cellular differentiation and a cellular transporter (FABP6 BA binding). No DE of genes was documented in descending colon biopsies. The two groups had similar rectal sensation.</p><p>Conclusion Though sharing clinical symptoms with IBS-D, BAD is associated with biological differences and mechanisms that have potential to enhance diagnosis and treatment targeting barrier dysfunction, inflammatory and microbial changes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “In patients with Rome III criteria of IBS-D”
- body site study.description · “stool dysbiosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44860951 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN44860951 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Minnesota |
| SAMN44860951 | health_condition | ibs | R1 | 0.90 | biosample_attr | IBSD_NoBAM |
| SAMN44860951 | health_condition_detail | IBSD_NoBAM | R1 | 0.90 | sample.attr.phenotype | IBSD_NoBAM |
| SAMN44860951 | latitude | 44.0121 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0121 N 92.4802 W |
| SAMN44860951 | location_locality | Rochester | R3 | 0.70 | paper.fulltext.methods | Mayo Clinic, Rochester, Minnesota, USA |
| SAMN44860951 | location_region | Minnesota | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Minnesota |
| SAMN44860951 | location_site | Mayo Clinic | R3 | 0.70 | paper.fulltext.methods | Mayo Clinic, Rochester, Minnesota, USA |
| SAMN44860951 | longitude | -92.4802 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0121 N 92.4802 W |
Sequencing
194 runs over 194 samples · mean 8.74 Gbp per run (median 8.54 Gbp, total 1,695.83 Gbp; 194 runs with a base count) · layout PAIRED 194 · platform ILLUMINA 194 · models Illumina NovaSeq 6000 (194) · 96% of runs with a Sandpiper profile · first public 2025-12-21
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1189133.csv.gz (5.5 KB) · parquet (77.5 KB) — all 194 samples, every field with route and confidence · PRJNA1189133_determinations.csv.gz (9.3 KB) — 1,746 evidence rows