Fecal microbiome in infants with cystic fibrosis
1,279 fecal samples from infants, mostly with cystic fibrosis and some healthy controls, in a longitudinal cohort study examining gut microbiome links to nutritional status. machine-written summary
1,279 samples · 1,279 runs · US · Infant / toddler · 2019 · 2.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,157 sample values (timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10769871, PMC11497992, PMC7018602, PMC8444586 |
| ✓ Supplementary tables | 1,401 sample values (country, subject id) |
| ✓ External resources | 6,146 sample values (age, antibiotic exposure, health condition, health condition detail, sex) · from GMrepo v3, MicrobiomeDB (VEuPathDB) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: supplementary table and MicrobiomeDB disagree for 122 samples (e.g. 1001 vs 456.6) — withheld; sex differs between samples of the same subject id (1 subjects, 2 samples) — sex withheld; subject ids shared by samples of both sexes (9 ids, 1157 samples) — ids withheld.
The sources disagree on 1,279 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 1,281)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN10615505 | age | 1001 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615506 | age | 1002 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615507 | age | 1001 (supplementary table) | 304.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615508 | age | 1002 (supplementary table) | 304.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615509 | age | 1002 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615510 | age | 1001 (supplementary table) | 761.0 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615511 | age | 1001 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615512 | age | 1002 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615513 | age | 1001 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615514 | age | 1003 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615515 | age | 1003 (supplementary table) | 761.0 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615516 | age | 1002 (supplementary table) | 761.0 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615517 | age | 1003 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615518 | age | 1004 (supplementary table) | 304.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615519 | age | 1003 (supplementary table) | 304.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615520 | age | 1003 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615521 | age | 1004 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615522 | age | 1004 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615523 | age | 1005 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615524 | age | 1006 (supplementary table) | 304.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615525 | age | 1004 (supplementary table) | 761.0 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615526 | age | 1005 (supplementary table) | 304.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615527 | age | 1006 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615528 | age | 1004 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615529 | age | 1005 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615530 | age | 1005 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615531 | age | 1005 (supplementary table) | 761.0 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615532 | age | 1007 (supplementary table) | 761.0 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615533 | age | 1007 (supplementary table) | 304.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615534 | age | 1007 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615535 | age | 1007 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615536 | age | 1007 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615537 | age | 1006 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615538 | age | 1008 (supplementary table) | 152.2 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615539 | age | 1006 (supplementary table) | 761.0 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615540 | age | 1006 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615541 | age | 1008 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615542 | age | 1009 (supplementary table) | 608.8 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615543 | age | 1008 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
| SAMN10615544 | age | 1009 (supplementary table) | 456.6 (MicrobiomeDB) | withheld: neither value published |
longitudinal — not resolved
5 of 5 people sampled more than once (122 samples; median 25, up to 25 per person). Schedule stated by the source: “Repeated stool sampling per child at monthly visits labeled M01 through M12 (not all months present per subject)”.
Genera, mean relative abundance over 1,152 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 | 1,279 | 100% | ||||
| country | 1,279 | 100% | 1,279 | |||
| health_condition | 1,279 | 100% | 1,279 | |||
| subject_id | 122 | 10% | 122 | |||
| health_condition_detail | 1,279 | 100% | 1,279 | |||
| antibiotic_exposure | 1,276 | 100% | 1,276 | |||
| age_at_collection_days | 1,157 | 90% | 1,157 | |||
| timepoint_label | 1,157 | 90% | 1,157 | |||
| sex | 1,155 | 90% | 1,155 |
- Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure. PMID 31959989 PMC7018602 curated
- Infants with cystic fibrosis have altered fecal functional capacities with potential clinical and metabolic consequences. PMID 34525965 PMC8444586 curated
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871 curated
- Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. PMID 39428758 PMC11497992 curated
Archive description
Microbes that live in the gastrointestinal tracts of humans and other animals play key roles in the metabolism of nutrients, harvest of energy for the host, and the uptake of vitamins. Therefore, these microbes may be important contributors to diseases in which nutrients are poorly absorbed, the gastrointestinal tract is diseased, and/or the host grows poorly. 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 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 · “The relationship of fecal microbiomes and nutritional”
- body site study.description · “live in the gastrointestinal tracts of humans”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “growth failure in children with the genetic”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10615592 | age_at_collection_days | 91.32 | R2 | 0.75 | external.microbiomedb source | Age: 3 months |
| SAMN10615505 | antibiotic_exposure | no | R2 | 0.75 | external.microbiomedb source | Antibiotic exposure: No |
| SAMN10615505 | country | US | R2 | 0.75 | paper.supp.table | Country=USA |
| SAMN10615505 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN10615505 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN10615592 | sex | female | R2 | 0.75 | external.gmrepo source | sex: Female |
| SAMN10615505 | subject_id | PRJNA510445_180 | R2 | 0.75 | paper.supp.table | Host ID=PRJNA510445_180 |
| SAMN10615592 | timepoint_label | M03 | R1 | 0.70 | sample.title | B645-M03 |
Sequencing
1,279 runs over 1,279 samples · mean 2.54 Gbp per run (median 2.42 Gbp, total 3,251.96 Gbp; 1,279 runs with a base count) · layout PAIRED 1,279 · platform ILLUMINA 1,279 · models Illumina HiSeq 2500 (795), Illumina HiSeq 2000 (484) · 90% of runs with a Sandpiper profile · first public 2019-11-14
Authors (41)
Hayden HS first · Eng A · Pope CE · Brittnacher MJ · Vo AT · Weiss EJ · Hager KR · Martin BD · Leung DH · Heltshe SL · Borenstein E · Miller SI · Hoffman LR last · Raftery D · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Minot SS first · Mayer-Blackwell K · Fiore-Gartland A · Johnson A · Self S · Bhatti P · Yao L · Liu L · Sun X · Jinfa Y · Kublin J last
Downloads
PRJNA510445.csv.gz (34.2 KB) · parquet (122.4 KB) — all 1,279 samples, every field with route and confidence · PRJNA510445_determinations.csv.gz (74.1 KB) — 8,704 evidence rows