Pediatric short bowel syndrome gut microbiota, Dallas, TX
Longitudinal study of 11 stool samples from children with short bowel syndrome and healthy controls in Dallas, Texas, comparing gut bacterial populations. machine-written summary
11 samples · 16 runs · US · Infant / toddler · 2016 · 12.48 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 44 sample values (collection date, country, health condition, health condition detail) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 11 sample values (antibiotic exposure) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
Schedule stated by the source: “Stool samples collected from children with SBS and healthy controls over a three month period” (time origin: enrolment); stated follow-up 3 mo.
Genera, mean relative abundance over 11 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 | 11 | 100% | 11 | |||
| health_condition | 11 | 100% | 11 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 11 | 100% | 11 | |||
| collection_date | 11 | 100% | 11 | |||
| health_condition_detail | 11 | 100% | 11 |
- Severe Gut Microbiota Dysbiosis Is Associated With Poor Growth in Patients With Short Bowel Syndrome. 2017 PMID 27406942 own_data
Archive description
This is a prospective cohort study using metagenomics to characterize gut microbiota populations of pediatric short bowel syndrome (SBS) patients with variable growth trajectories. Stool samples were collected from children with SBS and healthy controls over a three month period. Differences in gut bacterial populations were compared between healthy children and those with SBS (including a more in depth analysis of SBS children exhibiting poor and good growth).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Severe gut microbiota dysbiosis is”
- body site study.description · “metagenomics to characterize gut microbiota populations of”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “microbiota populations of pediatric short bowel syndrome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04480489 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN04480489 | collection_date | 2014-06-16 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2014-06-16 |
| SAMN04480489 | country | US | R1 | 0.90 | biosample_attr | USA: Dallas, Texas |
| SAMN04480489 | health_condition | healthy_control | R1 | 0.90 | sample.attr.condition | condition=Healthy |
| SAMN04480489 | health_condition_detail | Healthy | R1 | 0.90 | biosample.attribute:condition | condition: Healthy |
Sequencing
16 runs over 11 samples · mean 8.23 Gbp per run (median 6.00 Gbp, total 131.67 Gbp; 16 runs with a base count) · layout PAIRED 16 · platform ILLUMINA 16 · models Illumina HiSeq 2000 (16) · 100% of runs with a Sandpiper profile · first public 2016-07-16
Authors (11)
Piper HG first · Fan D · Coughlin LA · Ho EX · McDaniel MM · Channabasappa N · Kim J · Kim M · Zhan X · Xie Y · Koh AY last
Downloads
PRJNA311208.csv.gz (1.2 KB) · parquet (69.7 KB) — all 11 samples, every field with route and confidence · PRJNA311208_determinations.csv.gz (1.3 KB) — 55 evidence rows