Fecal microbiota in children with cystic fibrosis
Case-control study of 102 fecal samples from children with cystic fibrosis and healthy controls, examining gut microbiota (notably E. coli abundance) in relation to nutrient malabsorption and intestinal inflammation. machine-written summary
102 samples · 102 runs · US · Child · 2017 · 3.61 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 102 sample values (subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked · PMC3890337 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 306 sample values (country, health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
25 of 27 people sampled more than once (100 samples; median 4, up to 5 per person).
Genera, mean relative abundance over 88 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 | 102 | 100% | ||||
| country | 102 | 100% | 102 | |||
| health_condition | 102 | 100% | 102 | |||
| subject_id | 102 | 100% | 102 | |||
| health_condition_detail | 102 | 100% | 102 |
- Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis. 2014 PMID 24178246 PMC3890337 own_data
Archive description
The aim of this project is to determine the role of gastrointestinal microbes in the relentless and difficult-to-treat growth failure in children with the genetic disease cystic fibrosis, with the hope of both identifying interventions that will lead to better nutritional outcomes in these and in other children with poor early growth.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “children with the genetic disease cystic fibrosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05290535 | country | US | R2 | 0.75 | external.gmrepo source | country: United States of America |
| SAMN05290535 | health_condition | other_disease | R2 | 0.75 | external.gmrepo source | phenotype: Cystic Fibrosis |
| SAMN05290535 | health_condition_detail | Cystic Fibrosis | R2 | 0.75 | external.gmrepo source | phenotype: Cystic Fibrosis |
| SAMN05290535 | subject_id | CM101 | R1 | 0.70 | sample.name_rule:alias | CM101S3 |
Sequencing
102 runs over 102 samples · mean 4.07 Gbp per run (median 3.61 Gbp, total 414.72 Gbp; 102 runs with a base count) · layout PAIRED 67, SINGLE 35 · platform ILLUMINA 102 · models Illumina HiSeq 2000 (102) · 86% of runs with a Sandpiper profile · first public 2017-11-09
Authors (13)
Hoffman LR first · Pope CE · Hayden HS · Heltshe S · Levy R · McNamara S · Jacobs MA · Rohmer L · Radey M · Ramsey BW · Brittnacher MJ · Borenstein E · Miller SI last
Downloads
PRJNA314903.csv.gz (3.1 KB) · parquet (72.8 KB) — all 102 samples, every field with route and confidence · PRJNA314903_determinations.csv.gz (3.9 KB) — 408 evidence rows