Longitudinal faecal microbiota in IBS patients, Spain
7 faecal samples from adults with irritable bowel syndrome (diarrhoea subtype) in Spain, including a healthy relative as control, collected in a longitudinal design tracking microbiota over time. machine-written summary
7 samples · 7 runs · ES · Adult · 2013 · 0.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 98 sample values (age, bmi, collection date, country, diet, diet detail, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked · PMC3554406 |
| ○ 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
2 of 2 people sampled more than once (7 samples; median 4, up to 5 per person) · follow-up median 4 d (max 4 d) · median interval between samples 2 d (time from collection dates). Schedule stated by the source: “Faecal samples collected every two days the first week and then weekly over two months” (time origin: enrolment); stated follow-up 2 mo.
Each row is one person (2 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 7 | 100% | ||||
| country | 7 | 100% | 7 | |||
| health_condition | 7 | 100% | 7 | |||
| subject_id | 7 | 100% | 7 | |||
| age_at_collection_days | 7 | 100% | 7 | |||
| bmi | 7 | 100% | 7 | |||
| collection_date | 7 | 100% | 7 | |||
| detailed_location | 7 | 100% | ||||
| diet | 7 | 100% | 7 | |||
| diet_detail | 7 | 100% | 7 | |||
| health_condition_detail | 7 | 100% | 7 | |||
| latitude | 7 | 100% | 7 | |||
| location_region | 7 | 100% | 7 | |||
| longitude | 7 | 100% | 7 | |||
| sex | 7 | 100% | 7 | |||
| smoking_status | 7 | 100% | 7 |
- Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study. 2013 PMID 23038176 PMC3554406 own_data
Archive description
Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western countries. The definition and treatment of IBS is challenging due to its largely unknown aetiology and the variety of symptoms it can present. Previous studies on IBS suggest subtle alterations in the composition of intestinal microbiota. However, no consensus has been reached regarding the association between specific bacteria and IBS. To overcome the confusion introduced by inter-subject variability and heterogeneity within IBS that is problematic in cross-sectional studies, we undertook a longitudinal study that allowed us to compare samples from single patients at moments with different type and/or severity of symptoms. We present results for two IBS patients with diarrhoea subtype and the healthy relative of one of them. Faecal samples collected every two days the first week and then weekly over two months were analysed through metagenomic and metatranscriptomic approaches. Overall, we detect a greater instability of faecal microbiota in IBS patients when compared to the control, and even larger instability associated with acute diarrheoa. Bacterial composition and encoded functions were fairly stable throughout. On the contrary, the fraction of active bacteria varied markedly in time. Strong and quick compositional shifts were associated with relapse, although with low reproducibility between and within patients. Similarly, changes in the global pattern of gene expression characterized days of worsening, but we could not identify genes or functions associated with relapse. Our results confirm that the association of microbiota with IBS is rather weak.
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.title · “Follow-up of faecal microbiota in IBS”
- body site study.description · “most common functional gastrointestinal disorder in western”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA2164650 | age_at_collection_days | 7670.2 | R1 | 0.70 | sample.attr.age | 21 |
| SAMEA2164650 | bmi | 30.4 | R1 | 0.90 | sample.attr.body_mass_index | 30.4 |
| SAMEA2164650 | collection_date | 2010-07-02 | R1 | 0.90 | biosample.attribute:collection_date | 2010-07-02 |
| SAMEA2164650 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_region_area | Spain |
| SAMEA2164650 | diet | mediterranean | R1 | 0.90 | biosample.attribute:diet | mediterranean diet |
| SAMEA2164650 | diet_detail | mediterranean diet | R1 | 0.90 | biosample.attribute:diet | mediterranean diet |
| SAMEA2164650 | health_condition | ibs | R1 | 0.90 | biosample_attr | irritable bowel syndrome, diarrhoea subtype |
| SAMEA2164650 | health_condition_detail | bowel symptoms: presence of abdominal pain, abdominal distension and defecatory urgency; 11 stools (11 in form of diarrh | R1 | 0.90 | sample.attr.disease_status | bowel symptoms: presence of abdominal pain, abdominal distension and defecatory urgency; 11 |
| SAMEA2164650 | latitude | 39.4697 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.46972222222 -0.3775 |
| SAMEA2164650 | location_region | Valencia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.46972222222 -0.3775 |
| SAMEA2164650 | longitude | -0.3775 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.46972222222 -0.3775 |
| SAMEA2164650 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMEA2164650 | smoking_status | current | R1 | 0.90 | biosample.attribute:smoker | smoker |
| SAMEA2164650 | subject_id | P2 | R1 | 0.85 | sample.attr.host_subject_id | P2 |
Sequencing
7 runs over 7 samples · mean 0.15 Gbp per run (median 0.14 Gbp, total 1.03 Gbp; 7 runs with a base count) · layout SINGLE 7 · platform LS454 7 · models 454 GS FLX Titanium (7) · 0% of runs with a Sandpiper profile · first public 2013-07-31
Authors (5)
Bachy C first · Dolan JR · López-García P · Deschamps P · Moreira D last
Downloads
PRJEB3227.csv.gz (1.3 KB) · parquet (71.9 KB) — all 7 samples, every field with route and confidence · PRJEB3227_determinations.csv.gz (1.7 KB) — 98 evidence rows