Gut microbiome in IBS vs healthy Mexican adults
9 samples from adult Mestizo subjects in Mexico, comparing intestinal microbiota taxonomic composition between IBS patients and healthy controls in a case-control design. machine-written summary
9 samples · 9 runs · MX · Adult · 2020 · 19.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 45 sample values (age, collection date, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 27 sample values (antibiotic exposure, country, location site) · PMC7098960 |
| ○ 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 2 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 | 9 | 100% | ||||
| country | 9 | 100% | 9 | |||
| health_condition | 9 | 100% | 9 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 9 | 100% | 9 | |||
| antibiotic_exposure | 9 | 100% | 9 | |||
| collection_date | 9 | 100% | 9 | |||
| detailed_location | 9 | 100% | ||||
| health_condition_detail | 9 | 100% | 9 | |||
| location_site | 9 | 100% | 9 | |||
| sex | 9 | 100% | 9 |
- Mucosal Microbiome Profiles Polygenic Irritable Bowel Syndrome in Mestizo Individuals. 2020 PMID 32266159 PMC7098960 own_data
Archive description
Data of taxonomic composition of the intestinal microbiota in IBS patients and healthy subjects from Mexico.
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 · “composition of the intestinal microbiota in IBS”
- 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 |
|---|---|---|---|---|---|---|
| SAMN13087259 | age_at_collection_days | 21915.0 | R1 | 0.70 | sample.attr.host_age | 60 |
| SAMN13087259 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | excluded if they received antibiotics |
| SAMN13087259 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN13087259 | country | MX | R3 | 0.70 | paper.fulltext.methods | recruited at the Hospital General de México |
| SAMN13087259 | health_condition | ibs | R1 | 0.85 | biosample.attribute:gastrointest_disord | Irritable Bowel Syndrome |
| SAMN13087259 | health_condition_detail | biopsies | R1 | 0.90 | sample.attr.liver_disord | biopsies |
| SAMN13087259 | location_site | Hospital General de México Dr. Eduardo Liceaga | R3 | 0.70 | paper.fulltext.methods | recruited at the Hospital General de México Dr. Eduardo Liceaga |
| SAMN13087259 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
Sequencing
9 runs over 9 samples · mean 20.34 Gbp per run (median 19.20 Gbp, total 183.07 Gbp; 9 runs with a base count) · layout PAIRED 9 · platform ILLUMINA 9 · models Illumina HiSeq 4000 (9) · 78% of runs with a Sandpiper profile · first public 2020-10-01
Authors (13)
Arredondo-Hernández R first · Schmulson M · Orduña P · López-Leal G · Zarate AM · Alanis-Funes G · Alcaraz LD · Santiago-Cruz R · Cevallos MA · Villa AR · Ponce-de-León Rosales S · López-Vidal Y · Consorcio Mexicano para el Estudio del Microbioma Humano last
Downloads
PRJNA579180.csv.gz (1.2 KB) · parquet (70.4 KB) — all 9 samples, every field with route and confidence · PRJNA579180_determinations.csv.gz (1.2 KB) — 72 evidence rows